The fungus Ustilago maydis, from the aztec cuisine to the research laboratory.

PubMed

Ruiz-Herrera, J; Martínez-Espinoza, A D

1998-06-01

Ustilago maydis is a plant pathogen fungus responsible for corn smut. It has a complex life cycle. In its saprophitic stage, it grows as haploid yeast cells, while in the invasive stage it grows as a mycelium formed by diploid cells. Thus, a correlation exists between genetic ploidy, pathogenicity and morphogenesis. Dimorphism can be modulated in vitro by changing environmental parameters such as pH. Studies with auxotrophic mutants have shown that polyamines play a central role in regulating dimorphism. Molecular biology approaches are being employed for the analysis of fundamental aspects of the biology of this fungus, such as mating type regulation, dimorphism or cell wall biogenesis.

Characterization of ApB73, a virulence factor important for colonization of Zea mays by the smut Ustilago maydis

PubMed Central

Stirnberg, Alexandra

2016-01-01

Summary The biotrophic fungus Ustilago maydis, the causal agent of corn smut disease, uses numerous small secreted effector proteins to suppress plant defence responses and reshape the host metabolism. However, the role of specific effectors remains poorly understood. Here, we describe the identification of ApB73 (Apathogenic in B73), an as yet uncharacterized protein essential for the successful colonization of maize by U. maydis. We show that apB73 is transcriptionally induced during the biotrophic stages of the fungal life cycle. The deletion of the apB73 gene results in cultivar‐specific loss of gall formation in the host. The ApB73 protein is conserved among closely related smut fungi. However, using virulence assays, we show that only the orthologue of the maize‐infecting head smut Sporisorium reilianum can complement the mutant phenotype of U. maydis. Although microscopy shows that ApB73 is secreted into the biotrophic interface, it seems to remain associated with fungal cell wall components or the fungal plasma membrane. Taken together, the results show that ApB73 is a conserved and important virulence factor of U. maydis that localizes to the interface between the pathogen and its host Zea mays. PMID:27279632

A secreted Ustilago maydis effector promotes virulence by targeting anthocyanin biosynthesis in maize

PubMed Central

Tanaka, Shigeyuki; Brefort, Thomas; Neidig, Nina; Djamei, Armin; Kahnt, Jörg; Vermerris, Wilfred; Koenig, Stefanie; Feussner, Kirstin; Feussner, Ivo; Kahmann, Regine

2014-01-01

The biotrophic fungus Ustilago maydis causes smut disease in maize with characteristic tumor formation and anthocyanin induction. Here, we show that anthocyanin biosynthesis is induced by the virulence promoting secreted effector protein Tin2. Tin2 protein functions inside plant cells where it interacts with maize protein kinase ZmTTK1. Tin2 masks a ubiquitin–proteasome degradation motif in ZmTTK1, thus stabilizing the active kinase. Active ZmTTK1 controls activation of genes in the anthocyanin biosynthesis pathway. Without Tin2, enhanced lignin biosynthesis is observed in infected tissue and vascular bundles show strong lignification. This is presumably limiting access of fungal hyphae to nutrients needed for massive proliferation. Consistent with this assertion, we observe that maize brown midrib mutants affected in lignin biosynthesis are hypersensitive to U. maydis infection. We speculate that Tin2 rewires metabolites into the anthocyanin pathway to lower their availability for other defense responses. DOI: http://dx.doi.org/10.7554/eLife.01355.001 PMID:24473076

The Biotrophic Development of Ustilago maydis Studied by RNA-Seq Analysis[OPEN

PubMed Central

Lanver, Daniel; Müller, André N.; Happel, Petra; Franitza, Marek; Reissmann, Stefanie; Altmüller, Janine

2018-01-01

The maize smut fungus Ustilago maydis is a model organism for elucidating host colonization strategies of biotrophic fungi. Here, we performed an in depth transcriptional profiling of the entire plant-associated development of U. maydis wild-type strains. In our analysis, we focused on fungal metabolism, nutritional strategies, secreted effectors, and regulatory networks. Secreted proteins were enriched in three distinct expression modules corresponding to stages on the plant surface, establishment of biotrophy, and induction of tumors. These modules are likely the key determinants for U. maydis virulence. With respect to nutrient utilization, we observed that expression of several nutrient transporters was tied to these virulence modules rather than being controlled by nutrient availability. We show that oligopeptide transporters likely involved in nitrogen assimilation are important virulence factors. By measuring the intramodular connectivity of transcription factors, we identified the potential drivers for the virulence modules. While known components of the b-mating type cascade emerged as inducers for the plant surface and biotrophy module, we identified a set of yet uncharacterized transcription factors as likely responsible for expression of the tumor module. We demonstrate a crucial role for leaf tumor formation and effector gene expression for one of these transcription factors. PMID:29371439

The O-Mannosyltransferase PMT4 Is Essential for Normal Appressorium Formation and Penetration in Ustilago maydis[W][OA

PubMed Central

Fernández-Álvarez, Alfonso; Elías-Villalobos, Alberto; Ibeas, José I.

2009-01-01

In Saccharomyces cerevisiae, the PMT, KRE2/MNT1, and MNN1 mannosyltransferase protein families catalyze the steps of the O-mannosylation pathway, sequentially adding mannoses to target proteins. We have identified members of all three families and analyzed their roles in pathogenesis of the maize smut fungus Ustilago maydis. Furthermore, we have shown that PMT4, one of the three PMT family members in U. maydis, is essential for tumor formation in Zea mays. Significantly, PMT4 seems to be required only for pathogenesis and is dispensable for other aspects of the U. maydis life cycle. We subsequently show that the deletion of pmt4 results in a strong reduction in the frequency of appressorium formation, with the few appressoria that do form lacking the capacity to penetrate the plant cuticle. Our findings suggest that the O-mannosylation pathway plays a key role in the posttranslational modification of proteins involved in the pathogenic development of U. maydis. The fact that PMT homologs are not found in plants may open new avenues for the development of fungal control strategies. Moreover, the discovery of a highly specific requirement for a single O-mannosyltransferase should aid in the identification of the proteins directly involved in fungal plant penetration, thus leading to a better understanding of plant–fungi interactions. PMID:19880800

Characterization of ApB73, a virulence factor important for colonization of Zea mays by the smut Ustilago maydis.

PubMed

Stirnberg, Alexandra; Djamei, Armin

2016-12-01

The biotrophic fungus Ustilago maydis, the causal agent of corn smut disease, uses numerous small secreted effector proteins to suppress plant defence responses and reshape the host metabolism. However, the role of specific effectors remains poorly understood. Here, we describe the identification of ApB73 (Apathogenic in B73), an as yet uncharacterized protein essential for the successful colonization of maize by U. maydis. We show that apB73 is transcriptionally induced during the biotrophic stages of the fungal life cycle. The deletion of the apB73 gene results in cultivar-specific loss of gall formation in the host. The ApB73 protein is conserved among closely related smut fungi. However, using virulence assays, we show that only the orthologue of the maize-infecting head smut Sporisorium reilianum can complement the mutant phenotype of U. maydis. Although microscopy shows that ApB73 is secreted into the biotrophic interface, it seems to remain associated with fungal cell wall components or the fungal plasma membrane. Taken together, the results show that ApB73 is a conserved and important virulence factor of U. maydis that localizes to the interface between the pathogen and its host Zea mays. © 2016 THE AUTHORS. MOLECULAR PLANT PATHOLOGY PUBLISHED BY BRITISH SOCIETY FOR PLANT PATHOLOGY AND JOHN WILEY & SONS LTD.

Fungal Secretome Analysis via PepSAVI-MS: Identification of the Bioactive Peptide KP4 from Ustilago maydis

NASA Astrophysics Data System (ADS)

Kirkpatrick, Christine L.; Parsley, Nicole C.; Bartges, Tessa E.; Cooke, Madeline E.; Evans, Wilaysha S.; Heil, Lilian R.; Smith, Thomas J.; Hicks, Leslie M.

2018-05-01

Fungal secondary metabolites represent a rich and largely untapped source for bioactive molecules, including peptides with substantial structural diversity and pharmacological potential. As methods proceed to take a deep dive into fungal genomes, complimentary methods to identify bioactive components are required to keep pace with the expanding fungal repertoire. We developed PepSAVI-MS to expedite the search for natural product bioactive peptides and herein demonstrate proof-of-principle applicability of the pipeline for the discovery of bioactive peptides from fungal secretomes via identification of the antifungal killer toxin KP4 from Ustilago maydis P4. This work opens the door to investigating microbial secretomes with a new lens, and could have broad applications across human health, agriculture, and food safety. [Figure not available: see fulltext.

Fungal Secretome Analysis via PepSAVI-MS: Identification of the Bioactive Peptide KP4 from Ustilago maydis

NASA Astrophysics Data System (ADS)

Kirkpatrick, Christine L.; Parsley, Nicole C.; Bartges, Tessa E.; Cooke, Madeline E.; Evans, Wilaysha S.; Heil, Lilian R.; Smith, Thomas J.; Hicks, Leslie M.

2018-02-01

Fungal secondary metabolites represent a rich and largely untapped source for bioactive molecules, including peptides with substantial structural diversity and pharmacological potential. As methods proceed to take a deep dive into fungal genomes, complimentary methods to identify bioactive components are required to keep pace with the expanding fungal repertoire. We developed PepSAVI-MS to expedite the search for natural product bioactive peptides and herein demonstrate proof-of-principle applicability of the pipeline for the discovery of bioactive peptides from fungal secretomes via identification of the antifungal killer toxin KP4 from Ustilago maydis P4. This work opens the door to investigating microbial secretomes with a new lens, and could have broad applications across human health, agriculture, and food safety. [Figure not available: see fulltext.

The Ustilago maydis repetitive effector Rsp3 blocks the antifungal activity of mannose-binding maize proteins.

PubMed

Ma, Lay-Sun; Wang, Lei; Trippel, Christine; Mendoza-Mendoza, Artemio; Ullmann, Steffen; Moretti, Marino; Carsten, Alexander; Kahnt, Jörg; Reissmann, Stefanie; Zechmann, Bernd; Bange, Gert; Kahmann, Regine

2018-04-27

To cause disease in maize, the biotrophic fungus Ustilago maydis secretes a large arsenal of effector proteins. Here, we functionally characterize the repetitive effector Rsp3 (repetitive secreted protein 3), which shows length polymorphisms in field isolates and is highly expressed during biotrophic stages. Rsp3 is required for virulence and anthocyanin accumulation. During biotrophic growth, Rsp3 decorates the hyphal surface and interacts with at least two secreted maize DUF26-domain family proteins (designated AFP1 and AFP2). AFP1 binds mannose and displays antifungal activity against the rsp3 mutant but not against a strain constitutively expressing rsp3. Maize plants silenced for AFP1 and AFP2 partially rescue the virulence defect of rsp3 mutants, suggesting that blocking the antifungal activity of AFP1 and AFP2 by the Rsp3 effector is an important virulence function. Rsp3 orthologs are present in all sequenced smut fungi, and the ortholog from Sporisorium reilianum can complement the rsp3 mutant of U. maydis, suggesting a novel widespread fungal protection mechanism.

Insights into Host Cell Modulation and Induction of New Cells by the Corn Smut Ustilago maydis.

PubMed

Redkar, Amey; Matei, Alexandra; Doehlemann, Gunther

2017-01-01

Many filamentous fungal pathogens induce drastic modulation of host cells causing abnormal infectious structures such as galls, or tumors that arise as a result of re-programming in the original developmental cell fate of a colonized host cell. Developmental consequences occur predominantly with biotrophic phytopathogens. This suggests that these host structures result as an outcome of efficient defense suppression and intimate fungal-host interaction to suit the pathogen's needs for completion of its infection cycle. This mini-review mainly summarizes host cell re-programming that occurs in the Ustilago maydis - maize interaction, in which the pathogen deploys cell-type specific effector proteins with varying activities. The fungus senses the physiological status and identity of colonized host cells and re-directs the endogenous developmental program of its host. The disturbance of host cell physiology and cell fate leads to novel cell shapes, increased cell size, and/or the number of host cells. We particularly highlight the strategies of U. maydis to induce physiologically varied host organs to form the characteristic tumors in both vegetative and floral parts of maize.

Uniparental mitochondrial DNA inheritance is not affected in Ustilago maydis Δatg11 mutants blocked in mitophagy.

PubMed

Wagner-Vogel, Gaby; Lämmer, Frauke; Kämper, Jörg; Basse, Christoph W

2015-02-06

Maternal or uniparental inheritance (UPI) of mitochondria is generally observed in sexual eukaryotes, however, the underlying mechanisms are diverse and largely unknown. Recently, based on the use of mutants blocked in autophagy, it has been demonstrated that autophagy is required for strict maternal inheritance in the nematode Caenorhabditis elegans. Uniparental mitochondrial DNA (mtDNA) inheritance has been well documented for numerous fungal species, and in particular, has been shown to be genetically governed by the mating-type loci in the isogamous species Cryptococcus neoformans, Phycomyces blakesleeanus and Ustilago maydis. Previously, we have shown that the a2 mating-type locus gene lga2 is decisive for UPI during sexual development of U. maydis. In axenic culture, conditional overexpression of lga2 triggers efficient loss of mtDNA as well as mitophagy. To assess a functional relationship, we have investigated UPI in U. maydis Δatg11 mutants, which are blocked in mitophagy. This study has revealed that Δatg11 mutants are not affected in pathogenic development and this has allowed us to analyse UPI under comparable developmental conditions between mating-compatible wild-type and mutant strain combinations. Explicitly, we have examined two independent strain combinations that gave rise to different efficiencies of UPI. We demonstrate that in both cases UPI is atg11-independent, providing evidence that mitophagy is not critical for UPI in U. maydis, even under conditions of strict UPI. Until now, analysis of a role of mitophagy in UPI has not been reported for microbial species. Our study suggests that selective autophagy does not contribute to UPI in U. maydis, but is rather a consequence of selective mtDNA elimination in response to mitochondrial damage.

In Silico Analysis of the Structural and Biochemical Features of the NMD Factor UPF1 in Ustilago maydis.

PubMed

Martínez-Montiel, Nancy; Morales-Lara, Laura; Hernández-Pérez, Julio M; Martínez-Contreras, Rebeca D

2016-01-01

The molecular mechanisms regulating the accuracy of gene expression are still not fully understood. Among these mechanisms, Nonsense-mediated Decay (NMD) is a quality control process that detects post-transcriptionally abnormal transcripts and leads them to degradation. The UPF1 protein lays at the heart of NMD as shown by several structural and functional features reported for this factor mainly for Homo sapiens and Saccharomyces cerevisiae. This process is highly conserved in eukaryotes but functional diversity can be observed in various species. Ustilago maydis is a basidiomycete and the best-known smut, which has become a model to study molecular and cellular eukaryotic mechanisms. In this study, we performed in silico analysis to investigate the structural and biochemical properties of the putative UPF1 homolog in Ustilago maydis. The putative homolog for UPF1 was recognized in the annotated genome for the basidiomycete, exhibiting 66% identity with its human counterpart at the protein level. The known structural and functional domains characteristic of UPF1 homologs were also found. Based on the crystal structures available for UPF1, we constructed different three-dimensional models for umUPF1 in order to analyze the secondary and tertiary structural features of this factor. Using these models, we studied the spatial arrangement of umUPF1 and its capability to interact with UPF2. Moreover, we identified the critical amino acids that mediate the interaction of umUPF1 with UPF2, ATP, RNA and with UPF1 itself. Mutating these amino acids in silico showed an important effect over the native structure. Finally, we performed molecular dynamic simulations for UPF1 proteins from H. sapiens and U. maydis and the results obtained show a similar behavior and physicochemical properties for the protein in both organisms. Overall, our results indicate that the putative UPF1 identified in U. maydis shows a very similar sequence, structural organization, mechanical stability, physicochemical properties and spatial organization in comparison to the NMD factor depicted for Homo sapiens. These observations strongly support the notion that human and fungal UPF1 could perform equivalent biological activities.

Lipid droplets accumulation and other biochemical changes induced in the fungal pathogen Ustilago maydis under nitrogen-starvation.

PubMed

Aguilar, Lucero Romero; Pardo, Juan Pablo; Lomelí, Mónica Montero; Bocardo, Oscar Ivan Luqueño; Juárez Oropeza, Marco A; Guerra Sánchez, Guadalupe

2017-10-01

In many organisms, the growth under nitrogen-deprivation or a poor nitrogen source impacts on the carbon flow distribution and causes accumulation of neutral lipids, which are stored as lipid droplets (LDs). Efforts are in progress to find the mechanism of LDs synthesis and degradation, and new organisms capable of accumulating large amounts of lipids for biotechnological applications. In this context, when Ustilago maydis was cultured in the absence of a nitrogen source, there was a large accumulation of lipid bodies containing mainly triacylglycerols. The most abundant fatty acids in lipid bodies at the stationary phase were palmitic, linoleic, and oleic acids, and they were synthesized de novo by the fatty-acid synthase. In regard to the production of NADPH for the synthesis of fatty acids, the cytosolic NADP + -dependent isocitrate dehydrogenase and the glucose-6-phosphate and 6-phosphogluconate dehydrogenases couple showed the highest specific activities, with a lower activity of the malic enzyme. The ATP-citrate lyase activity was not detected in any of the culture conditions, which points to a different mechanism for the transfer of acetyl-CoA into the cytosol. Protein and RNA contents decreased when U. maydis was grown without a nitrogen source. Due to the significant accumulation of triacylglycerols and the particular composition of fatty acids, U. maydis can be considered an alternative model for biotechnological applications.

Genetic Evidence for the Action of Oxathiin and Thiazole Derivatives on the Succinic Dehydrogenase System of Ustilago maydis Mitochondria

PubMed Central

Georgopoulos, S. G.; Alexandri, E.; Chrysayi, M.

1972-01-01

The inhibitory effect of fungitoxic derivatives of 1,4-oxathiin on substrate oxidation by the basidiomycete Ustilago maydis is diminished by a single-gene mutation (oxr). The difference between mutant and wild type is approximately the same on the basis of inhibition of either growth and operation of the tricarboxylic acid cycle in intact cells or succinate-driven reduction of ferricyanide by mitochondrial preparations. The mutation affects the behavior of the succinic dehydrogenase system of mitochondria not only in the presence but also in the absence of the toxicant, from which it is concluded that some component of the system itself has been modified. The malonate and the antimycin A sensitivity of the oxr mutant is similar to that of the wild type but cross-resistance to thiazole derivatives is easily demonstrated. Images PMID:5030620

Transcriptomic analysis of the dimorphic transition of Ustilago maydis induced in vitro by a change in pH.

PubMed

Martínez-Soto, Domingo; Ruiz-Herrera, José

2013-01-01

Dimorphism is the property of fungi to grow as budding yeasts or mycelium, depending on the environmental conditions. This phenomenon is important as a model of differentiation in eukaryotic organisms, and since a large number of fungal diseases are caused by dimorphic fungi, its study is important for practical reasons. In this work, we examined the transcriptome during the dimorphic transition of the basidiomycota phytopathogenic fungus Ustilago maydis using microarrays, utilizing yeast and mycelium monomorphic mutants as controls. This way, we thereby identified 154 genes of the fungus that are specifically involved in the dimorphic transition induced by a pH change. Of these, 82 genes were up-regulated, and 72 were down-regulated. Differential categorization of these genes revealed that they mostly belonged to the classes of metabolism, cell cycle and DNA processing, transcription and protein fate, transport and cellular communication, stress, cell differentiation and biogenesis of cellular components, while a significant number of them corresponded to unclassified proteins. The data reported in this work are important for our understanding of the molecular bases of dimorphism in U. maydis, and possibly of other fungi. Copyright © 2013. Published by Elsevier Inc.

Galactose metabolism and toxicity in Ustilago maydis.

PubMed

Schuler, David; Höll, Christina; Grün, Nathalie; Ulrich, Jonas; Dillner, Bastian; Klebl, Franz; Ammon, Alexandra; Voll, Lars M; Kämper, Jörg

2018-05-01

In most organisms, galactose is metabolized via the Leloir pathway, which is conserved from bacteria to mammals. Utilization of galactose requires a close interplay of the metabolic enzymes, as misregulation or malfunction of individual components can lead to the accumulation of toxic intermediate compounds. For the phytopathogenic basidiomycete Ustilago maydis, galactose is toxic for wildtype strains, i.e. leads to growth repression despite the presence of favorable carbon sources as sucrose. The galactose sensitivity can be relieved by two independent modifications: (1) by disruption of Hxt1, which we identify as the major transporter for galactose, and (2) by a point mutation in the gene encoding the galactokinase Gal1, the first enzyme of the Leloir pathway. The mutation in gal1(Y67F) leads to reduced enzymatic activity of Gal1 and thus may limit the formation of putatively toxic galactose-1-phosphate. However, systematic deletions and double deletions of different genes involved in galactose metabolism point to a minor role of galactose-1-phosphate in galactose toxicity. Our results show that molecular triggers for galactose toxicity in U. maydis differ from yeast and mammals. Copyright © 2018 Elsevier Inc. All rights reserved.

Umchs5, a gene coding for a class IV chitin synthase in Ustilago maydis.

PubMed

Xoconostle-Cázares, B; Specht, C A; Robbins, P W; Liu, Y; León, C; Ruiz-Herrera, J

1997-12-01

A fragment corresponding to a conserved region of a fifth gene coding for chitin synthase in the plant pathogenic fungus Ustilago maydis was amplified by means of the polymerase chain reaction (PCR). The amplified fragment was utilized as a probe for the identification of the whole gene in a genomic library of the fungus. The predicted gene product of Umchs5 has highest similarity with class IV chitin synthases encoded by the CHS3 genes from Saccharomyces cerevisiae and Candida albicans, chs-4 from Neurospora crassa, and chsE from Aspergillus nidulans. Umchs5 null mutants were constructed by substitution of most of the coding sequence with the hygromycin B resistance cassette. Mutants displayed significant reduction in growth rate, chitin content, and chitin synthase activity, specially in the mycelial form. Virulence to corn plantules was also reduced in the mutants. PCR was also used to obtain a fragment of a sixth chitin synthase, Umchs6. It is suggested that multigenic control of chitin synthesis in U. maydis operates as a protection mechanism for fungal viability in which the loss of one activity is partially compensated by the remaining enzymes. Copyright 1997 Academic Press.

Defects in Mitochondrial and Peroxisomal β-Oxidation Influence Virulence in the Maize Pathogen Ustilago maydis

PubMed Central

Kretschmer, Matthias; Klose, Jana

2012-01-01

An understanding of metabolic adaptation during the colonization of plants by phytopathogenic fungi is critical for developing strategies to protect crops. Lipids are abundant in plant tissues, and fungal phytopathogens in the phylum basidiomycota possess both peroxisomal and mitochondrial β-oxidation pathways to utilize this potential carbon source. Previously, we demonstrated a role for the peroxisomal β-oxidation enzyme Mfe2 in the filamentous growth, virulence, and sporulation of the maize pathogen Ustilago maydis. However, mfe2 mutants still caused disease symptoms, thus prompting a more detailed investigation of β-oxidation. We now demonstrate that a defect in the had1 gene encoding hydroxyacyl coenzyme A dehydrogenase for mitochondrial β-oxidation also influences virulence, although its paralog, had2, makes only a minor contribution. Additionally, we identified a gene encoding a polypeptide with similarity to the C terminus of Mfe2 and designated it Mfe2b; this gene makes a contribution to virulence only in the background of an mfe2Δ mutant. We also show that short-chain fatty acids induce cell death in U. maydis and that a block in β-oxidation leads to toxicity, likely because of the accumulation of toxic intermediates. Overall, this study reveals that β-oxidation has a complex influence on the formation of disease symptoms by U. maydis that includes potential metabolic contributions to proliferation in planta and an effect on virulence-related morphogenesis. PMID:22707484

Ustilago maydis killer toxin as a new tool for the biocontrol of the wine spoilage yeast Brettanomyces bruxellensis.

PubMed

Santos, Antonio; Navascués, Eva; Bravo, Enrique; Marquina, Domingo

2011-01-31

Brettanomyces bruxellensis is one of the most damaging species for wine quality, and tools for controlling its growth are limited. In this study, thirty-nine strains belonging to Saccharomyces cerevisiae and B. bruxellensis have been isolated from wineries, identified and then tested against a panel of thirty-nine killer yeasts. Here, for the first time, the killer activity of Ustilago maydis is proven to be effective against B. bruxellensis. Mixed cultures in winemaking conditions show that U. maydis CYC 1410 has the ability to inhibit B. bruxellensis, while S. cerevisiae is fully resistant to its killer activity, indicating that it could be used in wine fermentation to avoid the development of B. bruxellensis without undesirable effects on the fermentative yeast. The characterization of the dsRNAs isolated and purified from U. maydis CYC 1410 indicated that this strain produces a KP6-related toxin. Killer toxin extracts were active against B. bruxellensis at pH values between 3.0 and 4.5 and temperatures comprised between 15 °C and 25 °C, confirming their biocontrol activity in winemaking and wine aging conditions. Furthermore, small amounts (100 AU/ml) of killer toxin extracts from U. maydis significantly reduced the amount of 4-ethylphenol produced by B. bruxellensis, indicating that in addition to the growth inhibition observed for high killer toxin concentrations (ranging from 400 to 2000 AU/ml), small amounts of the toxin are able to reduce the production of volatile phenols responsible for the aroma defects in wines caused by B. bruxellensis. Copyright © 2010 Elsevier B.V. All rights reserved.

A Secreted Effector Protein of Ustilago maydis Guides Maize Leaf Cells to Form Tumors

PubMed Central

Redkar, Amey; Hoser, Rafal; Schilling, Lena; Zechmann, Bernd; Krzymowska, Magdalena; Walbot, Virginia; Doehlemann, Gunther

2015-01-01

The biotrophic smut fungus Ustilago maydis infects all aerial organs of maize (Zea mays) and induces tumors in the plant tissues. U. maydis deploys many effector proteins to manipulate its host. Previously, deletion analysis demonstrated that several effectors have important functions in inducing tumor expansion specifically in maize leaves. Here, we present the functional characterization of the effector See1 (Seedling efficient effector1). See1 is required for the reactivation of plant DNA synthesis, which is crucial for tumor progression in leaf cells. By contrast, See1 does not affect tumor formation in immature tassel floral tissues, where maize cell proliferation occurs independent of fungal infection. See1 interacts with a maize homolog of SGT1 (Suppressor of G2 allele of skp1), a factor acting in cell cycle progression in yeast (Saccharomyces cerevisiae) and an important component of plant and human innate immunity. See1 interferes with the MAPK-triggered phosphorylation of maize SGT1 at a monocot-specific phosphorylation site. We propose that See1 interferes with SGT1 activity, resulting in both modulation of immune responses and reactivation of DNA synthesis in leaf cells. This identifies See1 as a fungal effector that directly and specifically contributes to the formation of leaf tumors in maize. PMID:25888589

The Transition from a Phytopathogenic Smut Ancestor to an Anamorphic Biocontrol Agent Deciphered by Comparative Whole-Genome Analysis[W][OPEN

PubMed Central

Lefebvre, François; Joly, David L.; Labbé, Caroline; Teichmann, Beate; Linning, Rob; Belzile, François; Bakkeren, Guus; Bélanger, Richard R.

2013-01-01

Pseudozyma flocculosa is related to the model plant pathogen Ustilago maydis yet is not a phytopathogen but rather a biocontrol agent of powdery mildews; this relationship makes it unique for the study of the evolution of plant pathogenicity factors. The P. flocculosa genome of ∼23 Mb includes 6877 predicted protein coding genes. Genome features, including hallmarks of pathogenicity, are very similar in P. flocculosa and U. maydis, Sporisorium reilianum, and Ustilago hordei. Furthermore, P. flocculosa, a strict anamorph, revealed conserved and seemingly intact mating-type and meiosis loci typical of Ustilaginales. By contrast, we observed the loss of a specific subset of candidate secreted effector proteins reported to influence virulence in U. maydis as the singular divergence that could explain its nonpathogenic nature. These results suggest that P. flocculosa could have once been a virulent smut fungus that lost the specific effectors necessary for host compatibility. Interestingly, the biocontrol agent appears to have acquired genes encoding secreted proteins not found in the compared Ustilaginales, including necrosis-inducing-Phytophthora-protein- and Lysin-motif- containing proteins believed to have direct relevance to its lifestyle. The genome sequence should contribute to new insights into the subtle genetic differences that can lead to drastic changes in fungal pathogen lifestyles. PMID:23800965

The Transcription Factor Rbf1 Is the Master Regulator for b-Mating Type Controlled Pathogenic Development in Ustilago maydis

PubMed Central

Vranes, Miroslav; Wahl, Ramon; Pothiratana, Chetsada; Schuler, David; Vincon, Volker; Finkernagel, Florian; Flor-Parra, Ignacio; Kämper, Jörg

2010-01-01

In the phytopathogenic basidiomycete Ustilago maydis, sexual and pathogenic development are tightly connected and controlled by the heterodimeric bE/bW transcription factor complex encoded by the b-mating type locus. The formation of the active bE/bW heterodimer leads to the formation of filaments, induces a G2 cell cycle arrest, and triggers pathogenicity. Here, we identify a set of 345 bE/bW responsive genes which show altered expression during these developmental changes; several of these genes are associated with cell cycle coordination, morphogenesis and pathogenicity. 90% of the genes that show altered expression upon bE/bW-activation require the zinc finger transcription factor Rbf1, one of the few factors directly regulated by the bE/bW heterodimer. Rbf1 is a novel master regulator in a multilayered network of transcription factors that facilitates the complex regulatory traits of sexual and pathogenic development. PMID:20700446

A Novel High-Affinity Sucrose Transporter Is Required for Virulence of the Plant Pathogen Ustilago maydis

PubMed Central

Goos, Sarah; Kämper, Jörg; Sauer, Norbert

2010-01-01

Plant pathogenic fungi cause massive yield losses and affect both quality and safety of food and feed produced from infected plants. The main objective of plant pathogenic fungi is to get access to the organic carbon sources of their carbon-autotrophic hosts. However, the chemical nature of the carbon source(s) and the mode of uptake are largely unknown. Here, we present a novel, plasma membrane-localized sucrose transporter (Srt1) from the corn smut fungus Ustilago maydis and its characterization as a fungal virulence factor. Srt1 has an unusually high substrate affinity, is absolutely sucrose specific, and allows the direct utilization of sucrose at the plant/fungal interface without extracellular hydrolysis and, thus, without the production of extracellular monosaccharides known to elicit plant immune responses. srt1 is expressed exclusively during infection, and its deletion strongly reduces fungal virulence. This emphasizes the central role of this protein both for efficient carbon supply and for avoidance of apoplastic signals potentially recognized by the host. PMID:20161717

Identification of O-mannosylated Virulence Factors in Ustilago maydis

PubMed Central

Fernández-Álvarez, Alfonso; Marín-Menguiano, Miriam; Lanver, Daniel; Jiménez-Martín, Alberto; Elías-Villalobos, Alberto; Pérez-Pulido, Antonio J.; Kahmann, Regine; Ibeas, José I.

2012-01-01

The O-mannosyltransferase Pmt4 has emerged as crucial for fungal virulence in the animal pathogens Candida albicans or Cryptococcus neoformans as well as in the phytopathogenic fungus Ustilago maydis. Pmt4 O-mannosylates specific target proteins at the Endoplasmic Reticulum. Therefore a deficient O-mannosylation of these target proteins must be responsible for the loss of pathogenicity in pmt4 mutants. Taking advantage of the characteristics described for Pmt4 substrates in Saccharomyces cerevisiae, we performed a proteome-wide bioinformatic approach to identify putative Pmt4 targets in the corn smut fungus U. maydis and validated Pmt4-mediated glycosylation of candidate proteins by electrophoretic mobility shift assays. We found that the signalling mucin Msb2, which regulates appressorium differentiation upstream of the pathogenicity-related MAP kinase cascade, is O-mannosylated by Pmt4. The epistatic relationship of pmt4 and msb2 showed that both are likely to act in the same pathway. Furthermore, constitutive activation of the MAP kinase cascade restored appressorium development in pmt4 mutants, suggesting that during the initial phase of infection the failure to O-mannosylate Msb2 is responsible for the virulence defect of pmt4 mutants. On the other hand we demonstrate that during later stages of pathogenic development Pmt4 affects virulence independently of Msb2, probably by modifying secreted effector proteins. Pit1, a protein required for fungal spreading inside the infected leaf, was also identified as a Pmt4 target. Thus, O-mannosylation of different target proteins affects various stages of pathogenic development in U. maydis. PMID:22416226

Two members of the Ustilago maydis velvet family influence teliospore development and virulence on maize seedlings.

PubMed

Karakkat, Brijesh B; Gold, Scott E; Covert, Sarah F

2013-12-01

Members of the fungal-specific velvet protein family regulate sexual and asexual spore production in the Ascomycota. We predicted, therefore, that velvet homologs in the basidiomycetous plant pathogen Ustilago maydis would regulate sexual spore development, which is also associated with plant disease progression in this fungus. To test this hypothesis, we studied the function of three U. maydis velvet genes, umv1, umv2 and umv3. Using a gene replacement strategy, deletion mutants were made in all three genes in compatible haploid strains, and additionally for umv1 and umv2 in the solopathogenic strain, SG200. None of the mutants showed novel morphological phenotypes during yeast-like, in vitro growth. However, the Δumv1 mutants failed to induce galls or teliospores in maize. Chlorazol black E staining of leaves infected with Δumv1 dikaryons revealed that the Δumv1 hyphae did not proliferate normally and were blocked developmentally before teliospore formation. The Δumv2 mutants were able to induce galls and teliospores in maize, but were slow to do so and thus reduced in virulence. The Δumv3 mutants were not affected in teliospore formation or disease progression. Complementation of the Δumv1 and Δumv2 mutations in the SG200 background produced disease indices similar to those of SG200. These results indicate that two U. maydis velvet family members, umv1 and umv2, are important for normal teliospore development and disease progression in maize seedlings. Copyright © 2013 Elsevier Inc. All rights reserved.

Three regulators of G protein signaling differentially affect mating, morphology and virulence in the smut fungus Ustilago maydis.

PubMed

Moretti, Marino; Wang, Lei; Grognet, Pierre; Lanver, Daniel; Link, Hannes; Kahmann, Regine

2017-09-01

Regulators of G protein signaling (RGS) proteins modulate heterotrimeric G protein signaling negatively. To broaden an understanding of the roles of RGS proteins in fungal pathogens, we functionally characterized the three RGS protein-encoding genes (rgs1, rgs2 and rgs3) in the phytopathogenic fungus Ustilago maydis. It was found that RGS proteins played distinct roles in the regulation of development and virulence. rgs1 had a minor role in virulence when deleted in a solopathogenic strain. In crosses, rgs1 was dispensable for mating and filamentation, but was required for teliospore production. Haploid rgs2 mutants were affected in cell morphology, growth, mating and were unable to cause disease symptoms in crosses. However, virulence was unaffected when rgs2 was deleted in a solopathogenic strain, suggesting an exclusive involvement in pre-fusion events. These rgs2 phenotypes are likely connected to elevated intracellular cAMP levels. rgs3 mutants were severely attenuated in mating, in their response to pheromone, virulence and formation of mature teliospores. The mating defect could be traced back to reduced expression of the transcription factor rop1. It was speculated that the distinct roles of the three U. maydis RGS proteins were achieved by direct modulation of the Gα subunit-activated signaling pathways as well as through Gα-independent functions. © 2017 John Wiley & Sons Ltd.

The Ustilago maydis Effector Pep1 Suppresses Plant Immunity by Inhibition of Host Peroxidase Activity

PubMed Central

Zechmann, Bernd; Hillmer, Morten; Doehlemann, Gunther

2012-01-01

The corn smut Ustilago maydis establishes a biotrophic interaction with its host plant maize. This interaction requires efficient suppression of plant immune responses, which is attributed to secreted effector proteins. Previously we identified Pep1 (Protein essential during penetration-1) as a secreted effector with an essential role for U. maydis virulence. pep1 deletion mutants induce strong defense responses leading to an early block in pathogenic development of the fungus. Using cytological and functional assays we show that Pep1 functions as an inhibitor of plant peroxidases. At sites of Δpep1 mutant penetrations, H2O2 strongly accumulated in the cell walls, coinciding with a transcriptional induction of the secreted maize peroxidase POX12. Pep1 protein effectively inhibited the peroxidase driven oxidative burst and thereby suppresses the early immune responses of maize. Moreover, Pep1 directly inhibits peroxidases in vitro in a concentration-dependent manner. Using fluorescence complementation assays, we observed a direct interaction of Pep1 and the maize peroxidase POX12 in vivo. Functional relevance of this interaction was demonstrated by partial complementation of the Δpep1 mutant defect by virus induced gene silencing of maize POX12. We conclude that Pep1 acts as a potent suppressor of early plant defenses by inhibition of peroxidase activity. Thus, it represents a novel strategy for establishing a biotrophic interaction. PMID:22589719

Identification of a Gene Cluster for Biosynthesis of Mannosylerythritol Lipids in the Basidiomycetous Fungus Ustilago maydis

PubMed Central

Hewald, Sandra; Linne, Uwe; Scherer, Mario; Marahiel, Mohamed A.; Kämper, Jörg; Bölker, Michael

2006-01-01

Many microorganisms produce surface-active substances that enhance the availability of water-insoluble substrates. Although many of these biosurfactants have interesting potential applications, very little is known about their biosynthesis. The basidiomycetous fungus Ustilago maydis secretes large amounts of mannosylerythritol lipids (MELs) under conditions of nitrogen starvation. We recently described a putative glycosyltransferase, Emt1, which is essential for MEL biosynthesis and whose expression is strongly induced by nitrogen limitation. We used DNA microarray analysis to identify additional genes involved in MEL biosynthesis. Here we show that emt1 is part of a gene cluster which comprises five open reading frames. Three of the newly identified proteins, Mac1, Mac2, and Mat1, contain short sequence motifs characteristic for acyl- and acetyltransferases. Mutational analysis revealed that Mac1 and Mac2 are essential for MEL production, which suggests that they are involved in the acylation of mannosylerythritol. Deletion of mat1 resulted in the secretion of completely deacetylated MELs, as determined by mass spectrometry. We overexpressed Mat1 in Escherichia coli and demonstrated that this enzyme acts as an acetyl coenzyme A-dependent acetyltransferase. Remarkably, Mat1 displays relaxed regioselectivity and is able to acetylate mannosylerythritol at both the C-4 and C-6 hydroxyl groups. Based on these results, we propose a biosynthesis pathway for the generation of mannosylerythritol lipids in U. maydis. PMID:16885300

Genome Comparison of Barley and Maize Smut Fungi Reveals Targeted Loss of RNA Silencing Components and Species-Specific Presence of Transposable Elements[W

PubMed Central

Laurie, John D.; Ali, Shawkat; Linning, Rob; Mannhaupt, Gertrud; Wong, Philip; Güldener, Ulrich; Münsterkötter, Martin; Moore, Richard; Kahmann, Regine; Bakkeren, Guus; Schirawski, Jan

2012-01-01

Ustilago hordei is a biotrophic parasite of barley (Hordeum vulgare). After seedling infection, the fungus persists in the plant until head emergence when fungal spores develop and are released from sori formed at kernel positions. The 26.1-Mb U. hordei genome contains 7113 protein encoding genes with high synteny to the smaller genomes of the related, maize-infecting smut fungi Ustilago maydis and Sporisorium reilianum but has a larger repeat content that affected genome evolution at important loci, including mating-type and effector loci. The U. hordei genome encodes components involved in RNA interference and heterochromatin formation, normally involved in genome defense, that are lacking in the U. maydis genome due to clean excision events. These excision events were possibly a result of former presence of repetitive DNA and of an efficient homologous recombination system in U. maydis. We found evidence of repeat-induced point mutations in the genome of U. hordei, indicating that smut fungi use different strategies to counteract the deleterious effects of repetitive DNA. The complement of U. hordei effector genes is comparable to the other two smuts but reveals differences in family expansion and clustering. The availability of the genome sequence will facilitate the identification of genes responsible for virulence and evolution of smut fungi on their respective hosts. PMID:22623492

Genome comparison of barley and maize smut fungi reveals targeted loss of RNA silencing components and species-specific presence of transposable elements.

PubMed

Laurie, John D; Ali, Shawkat; Linning, Rob; Mannhaupt, Gertrud; Wong, Philip; Güldener, Ulrich; Münsterkötter, Martin; Moore, Richard; Kahmann, Regine; Bakkeren, Guus; Schirawski, Jan

2012-05-01

Ustilago hordei is a biotrophic parasite of barley (Hordeum vulgare). After seedling infection, the fungus persists in the plant until head emergence when fungal spores develop and are released from sori formed at kernel positions. The 26.1-Mb U. hordei genome contains 7113 protein encoding genes with high synteny to the smaller genomes of the related, maize-infecting smut fungi Ustilago maydis and Sporisorium reilianum but has a larger repeat content that affected genome evolution at important loci, including mating-type and effector loci. The U. hordei genome encodes components involved in RNA interference and heterochromatin formation, normally involved in genome defense, that are lacking in the U. maydis genome due to clean excision events. These excision events were possibly a result of former presence of repetitive DNA and of an efficient homologous recombination system in U. maydis. We found evidence of repeat-induced point mutations in the genome of U. hordei, indicating that smut fungi use different strategies to counteract the deleterious effects of repetitive DNA. The complement of U. hordei effector genes is comparable to the other two smuts but reveals differences in family expansion and clustering. The availability of the genome sequence will facilitate the identification of genes responsible for virulence and evolution of smut fungi on their respective hosts.

The Ustilago maydis Nit2 Homolog Regulates Nitrogen Utilization and Is Required for Efficient Induction of Filamentous Growth

PubMed Central

Horst, Robin J.; Zeh, Christine; Saur, Alexandra; Sonnewald, Sophia; Sonnewald, Uwe

2012-01-01

Nitrogen catabolite repression (NCR) is a regulatory strategy found in microorganisms that restricts the utilization of complex and unfavored nitrogen sources in the presence of favored nitrogen sources. In fungi, this concept has been best studied in yeasts and filamentous ascomycetes, where the GATA transcription factors Gln3p and Gat1p (in yeasts) and Nit2/AreA (in ascomycetes) constitute the main positive regulators of NCR. The reason why functional Nit2 homologs of some phytopathogenic fungi are required for full virulence in their hosts has remained elusive. We have identified the Nit2 homolog in the basidiomycetous phytopathogen Ustilago maydis and show that it is a major, but not the exclusive, positive regulator of nitrogen utilization. By transcriptome analysis of sporidia grown on artificial media devoid of favored nitrogen sources, we show that only a subset of nitrogen-responsive genes are regulated by Nit2, including the Gal4-like transcription factor Ton1 (a target of Nit2). Ustilagic acid biosynthesis is not under the control of Nit2, while nitrogen starvation-induced filamentous growth is largely dependent on functional Nit2. nit2 deletion mutants show the delayed initiation of filamentous growth on maize leaves and exhibit strongly compromised virulence, demonstrating that Nit2 is required to efficiently initiate the pathogenicity program of U. maydis. PMID:22247264

Contributions of recombination and repair proteins to telomere maintenance in telomerase-positive and negative Ustilago maydis.

PubMed

Yu, Eun Young; Hsu, Min; Holloman, William K; Lue, Neal F

2018-01-01

Homologous recombination and repair factors are known to promote both telomere replication and recombination-based telomere extension. Herein, we address the diverse contributions of several recombination/repair proteins to telomere maintenance in Ustilago maydis, a fungus that bears strong resemblance to mammals with respect to telomere regulation and recombination mechanisms. In telomerase-positive U. maydis, deletion of rad51 and blm separately caused shortened but stably maintained telomeres, whereas deletion of both engendered similar telomere loss, suggesting that the repair proteins help to resolve similar problems in telomere replication. In telomerase-negative cells, the loss of Rad51 or Brh2 caused accelerated senescence and failure to generate survivors on semi-solid medium. However, slow growing survivors can be isolated through continuous liquid culturing, and these survivors exhibit type II-like as well as ALT-like telomere features. In contrast, the trt1Δ blmΔ double mutant gives rise to survivors as readily as the trt1Δ single mutant, and like the single mutant survivors, exhibit almost exclusively type I-like telomere features. In addition, we observed direct physical interactions between Blm and two telomere-binding proteins, which may thus recruit or regulate Blm at telomeres. Our findings provide the basis for further analyzing the interplays between telomerase, telomere replication, and telomere recombination. © 2017 John Wiley & Sons Ltd.

The WOPR Protein Ros1 Is a Master Regulator of Sporogenesis and Late Effector Gene Expression in the Maize Pathogen Ustilago maydis

PubMed Central

Tollot, Marie; Assmann, Daniela; Becker, Christian; Altmüller, Janine; Dutheil, Julien Y.; Wegner, Carl-Eric; Kahmann, Regine

2016-01-01

The biotrophic basidiomycete fungus Ustilago maydis causes smut disease in maize. Hallmarks of the disease are large tumors that develop on all aerial parts of the host in which dark pigmented teliospores are formed. We have identified a member of the WOPR family of transcription factors, Ros1, as major regulator of spore formation in U. maydis. ros1 expression is induced only late during infection and hence Ros1 is neither involved in plant colonization of dikaryotic fungal hyphae nor in plant tumor formation. However, during late stages of infection Ros1 is essential for fungal karyogamy, massive proliferation of diploid fungal cells and spore formation. Premature expression of ros1 revealed that Ros1 counteracts the b-dependent filamentation program and induces morphological alterations resembling the early steps of sporogenesis. Transcriptional profiling and ChIP-seq analyses uncovered that Ros1 remodels expression of about 30% of all U. maydis genes with 40% of these being direct targets. In total the expression of 80 transcription factor genes is controlled by Ros1. Four of the upregulated transcription factor genes were deleted and two of the mutants were affected in spore development. A large number of b-dependent genes were differentially regulated by Ros1, suggesting substantial changes in this regulatory cascade that controls filamentation and pathogenic development. Interestingly, 128 genes encoding secreted effectors involved in the establishment of biotrophic development were downregulated by Ros1 while a set of 70 “late effectors” was upregulated. These results indicate that Ros1 is a master regulator of late development in U. maydis and show that the biotrophic interaction during sporogenesis involves a drastic shift in expression of the fungal effectome including the downregulation of effectors that are essential during early stages of infection. PMID:27332891

The short form of the recombinant CAL-A-type lipase UM03410 from the smut fungus Ustilago maydis exhibits an inherent trans-fatty acid selectivity.

PubMed

Brundiek, Henrike; Saß, Stefan; Evitt, Andrew; Kourist, Robert; Bornscheuer, Uwe T

2012-04-01

The Ustilago maydis lipase UM03410 belongs to the mostly unexplored Candida antarctica lipase (CAL-A) subfamily. The two lipases with [corrected] the highest identity are a lipase from Sporisorium reilianum and the prototypic CAL-A. In contrast to the other CAL-A-type lipases, this hypothetical U. maydis lipase is annotated to possess a prolonged N-terminus of unknown function. Here, we show for the first time the recombinant expression of two versions of lipase UM03410: the full-length form (lipUMf) and an Nterminally truncated form (lipUMs). For comparison to the prototype, the expression of recombinant CAL-A in E. coli was investigated. Although both forms of lipase UM03410 could be expressed functionally in E. coli, the N-terminally truncated form (lipUMs) demonstrated significantly higher activities towards p-nitrophenyl esters. The functional expression of the N-terminally truncated lipase was further optimized by the appropriate choice of the E. coli strain, lowering the cultivation temperature to 20 °C and enrichment of the cultivation medium with glucose. Primary characteristics of the recombinant lipase are its pH optimum in the range of 6.5-7.0 and its temperature optimum at 55 °C. As is typical for lipases, lipUM03410 shows preference for long chain fatty acid esters with myristic acid ester (C14:0 ester) being the most preferred one.More importantly, lipUMs exhibits an inherent preference for C18:1Δ9 trans and C18:1Δ11 trans-fatty acid esters similar to CAL-A. Therefore, the short form of this U. maydis lipase is the only other currently known lipase with a distinct trans-fatty acid selectivity.

Physical and genetic interaction between ammonium transporters and the signaling protein Rho1 in the plant pathogen Ustilago maydis.

PubMed

Paul, Jinny A; Barati, Michelle T; Cooper, Michael; Perlin, Michael H

2014-10-01

Dimorphic transitions between yeast-like and filamentous forms occur in many fungi and are often associated with pathogenesis. One of the cues for such a dimorphic switch is the availability of nutrients. Under conditions of nitrogen limitation, fungal cells (such as those of Saccharomyces cerevisiae and Ustilago maydis) switch from budding to pseudohyphal or filamentous growth. Ammonium transporters (AMTs) are responsible for uptake and, in some cases, for sensing the availability of ammonium, a preferred nitrogen source. Homodimer and/or heterodimer formation may be required for regulating the activity of the AMTs. To investigate the potential interactions of Ump1 and Ump2, the AMTs of the maize pathogen U. maydis, we first used the split-ubiquitin system, followed by a modified split-YFP (yellow fluorescent protein) system, to validate the interactions in vivo. This analysis showed the formation of homo- and hetero-oligomers by Ump1 and Ump2. We also demonstrated the interaction of the high-affinity ammonium transporter, Ump2, with the Rho1 GTPase, a central protein in signaling, with roles in controlling polarized growth. This is the first demonstration in eukaryotes of the physical interaction in vivo of an ammonium transporter with the signaling protein Rho1. Moreover, the Ump proteins interact with Rho1 during the growth of cells in low ammonium concentrations, a condition required for the expression of the Umps. Based on these results and the genetic evidence for the interaction of Ump2 with both Rho1 and Rac1, another small GTPase, we propose a model for the role of these interactions in controlling filamentation, a fundamental aspect of development and pathogenesis in U. maydis. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Phenolic Compounds, Antioxidant Activity and Lipid Profile of Huitlacoche Mushroom (Ustilago maydis) Produced in Several Maize Genotypes at Different Stages of Development.

PubMed

Valdez-Morales, Maribel; Carlos, L Céspedes; Valverde, María Elena; Ramírez-Chávez, Enrique; Paredes-López, Octavio

2016-12-01

Huitlacoche mushroom (composed by the fruiting bodies growing on the maize ears from the basidiomycete Ustilago maydis) is a culinary delicacy with a great economic and nutraceutical value. In this work, phenolic content, antioxidant activity, ergosterol and fatty acids profile from huitlacoche produced in 15 creole and in one hybrid maize genotypes, and harvested at different stages of development were determined. The hybrid crop was studied in raw and cooked samples. Total phenolic content ranged from 415.6 to 921.8.0 mg gallic acid equivalents per 100 g of flour. Samples exhibited attractive antioxidant activities: 75 % of antiradical activity on average by DPPH methodology, and ORAC values up to 7661.3 μmol Trolox equivalents /100  g. Important quantities of ferulic acid, quercetin, ergosterol, linoleic and oleic acids were observed. Stage of development and cooking process had an effect on evaluated compounds, sometimes negative and sometimes positive. Results suggest that huitlacoche is an attractive food source of phenolics with excellent antioxidant potential and interesting lipidic compounds.

Dynein-mediated pulling forces drive rapid mitotic spindle elongation in Ustilago maydis

PubMed Central

Fink, Gero; Schuchardt, Isabel; Colombelli, Julien; Stelzer, Ernst; Steinberg, Gero

2006-01-01

Spindle elongation segregates chromosomes and occurs in anaphase, an essential step in mitosis. Dynein-mediated pulling forces position the spindle, but their role in anaphase is a matter of debate. Here, we demonstrate that dynein is responsible for rapid spindle elongation in the model fungus Ustilago maydis. We show that initial slow elongation is supported by kinesin-5, which is located in the spindle mid-zone. When the spindle reaches ∼2 μm in length, the elongation rate increases four-fold. This coincides with the appearance of long and less-dynamic microtubules (MTs) at each pole that accumulate dynein at their tips. Laser-mediated nanosurgery revealed that these MTs exert pulling forces in control cells, but not in dynein mutants. In addition, dynein mutants undergo initial slow anaphase, but fail to establish less-dynamic MTs and do not perform rapid spindle elongation, suggesting that dynein drives anaphase B. This is most likely mediated by cortical sliding of astral MTs along stationary dynein, which is off-loaded from the MT plus-end to the cortex. PMID:17024185

Evidence for a Ustilago maydis Steroid 5α-Reductase by Functional Expression in Arabidopsis det2-1 Mutants1

PubMed Central

Basse, Christoph W.; Kerschbamer, Christine; Brustmann, Markus; Altmann, Thomas; Kahmann, Regine

2002-01-01

We have identified a gene (udh1) in the basidiomycete Ustilago maydis that is induced during the parasitic interaction with its host plant maize (Zea mays). udh1 encodes a protein with high similarity to mammalian and plant 5α-steroid reductases. Udh1 differs from those of known 5α-steroid reductases by six additional domains, partially predicted to be membrane-spanning. A fusion protein of Udh1 and the green fluorescent protein provided evidence for endoplasmic reticulum localization in U. maydis. The function of the Udh1 protein was demonstrated by complementing Arabidopsis det2-1 mutants, which display a dwarf phenotype due to a mutation in the 5α-steroid reductase encoding DET2 gene. det2-1 mutant plants expressing either the udh1 or the DET2 gene controlled by the cauliflower mosaic virus 35S promoter differed from wild-type Columbia plants by accelerated stem growth, flower and seed development and a reduction in size and number of rosette leaves. The accelerated growth phenotype of udh1 transgenic plants was stably inherited and was favored under reduced light conditions. Truncation of the N-terminal 70 amino acids of the Udh1 protein abolished the ability to restore growth in det2-1 plants. Our results demonstrate the existence of a 5α-steroid reductase encoding gene in fungi and suggest a common ancestor between fungal, plant, and mammalian proteins. PMID:12068114

Evidence for a Ustilago maydis steroid 5alpha-reductase by functional expression in Arabidopsis det2-1 mutants.

PubMed

Basse, Christoph W; Kerschbamer, Christine; Brustmann, Markus; Altmann, Thomas; Kahmann, Regine

2002-06-01

We have identified a gene (udh1) in the basidiomycete Ustilago maydis that is induced during the parasitic interaction with its host plant maize (Zea mays). udh1 encodes a protein with high similarity to mammalian and plant 5alpha-steroid reductases. Udh1 differs from those of known 5alpha-steroid reductases by six additional domains, partially predicted to be membrane-spanning. A fusion protein of Udh1 and the green fluorescent protein provided evidence for endoplasmic reticulum localization in U. maydis. The function of the Udh1 protein was demonstrated by complementing Arabidopsis det2-1 mutants, which display a dwarf phenotype due to a mutation in the 5alpha-steroid reductase encoding DET2 gene. det2-1 mutant plants expressing either the udh1 or the DET2 gene controlled by the cauliflower mosaic virus 35S promoter differed from wild-type Columbia plants by accelerated stem growth, flower and seed development and a reduction in size and number of rosette leaves. The accelerated growth phenotype of udh1 transgenic plants was stably inherited and was favored under reduced light conditions. Truncation of the N-terminal 70 amino acids of the Udh1 protein abolished the ability to restore growth in det2-1 plants. Our results demonstrate the existence of a 5alpha-steroid reductase encoding gene in fungi and suggest a common ancestor between fungal, plant, and mammalian proteins.

An unusual MAP kinase is required for efficient penetration of the plant surface by Ustilago maydis

PubMed Central

Brachmann, Andreas; Schirawski, Jan; Müller, Philip; Kahmann, Regine

2003-01-01

In Ustilago maydis, pathogenic development is controlled by a heterodimer of the two homeodomain proteins bW and bE. We have identified by RNA fingerprinting a b-regulated gene, kpp6, which encodes an unusual MAP kinase. Kpp6 is similar to a number of other fungal MAP kinases involved in mating and pathogenicity, but contains an additional N-terminal domain unrelated to other proteins. Transcription of the kpp6 gene yields two transcripts differing in length, but encoding proteins of identical mass. One transcript is upregulated by the bW/bE heterodimer, while the other is induced after pheromone stimulation. kpp6 deletion mutants are attenuated in pathogenicity. kpp6T355A,Y357F mutants carrying a non-activatable allele of kpp6 are more severely compromised in pathogenesis. These strains can still form appressoria, but are defective in the subsequent penetration of the plant cuticle. Kpp6 is expressed during all stages of the sexual life cycle except mature spores. We speculate that Kpp6 may respond to a plant signal and regulate the genes necessary for efficient penetration of plant tissue. PMID:12727886

Heterologous production and characterization of a chlorogenic acid esterase from Ustilago maydis with a potential use in baking.

PubMed

Nieter, Annabel; Kelle, Sebastian; Takenberg, Meike; Linke, Diana; Bunzel, Mirko; Popper, Lutz; Berger, Ralf G

2016-10-15

Ustilago maydis, an edible mushroom growing on maize (Zea mays), is consumed as the food delicacy huitlacoche in Mexico. A chlorogenic acid esterase from this basidiomycete was expressed in good yields cultivating the heterologous host Pichia pastoris on the 5L bioreactor scale (reUmChlE; 45.9UL(-1)). In contrast to previously described chlorogenic acid esterases, the reUmChlE was also active towards feruloylated saccharides. The enzyme preferred substrates with the ferulic acid esterified to the O-5 position of arabinose residues, typical of graminaceous monocots, over the O-2 position of arabinose or the O-6 position of galactose residues. Determination of kcat/Km showed that the reUmChlE hydrolyzed chlorogenic acid 18-fold more efficiently than methyl ferulate, p-coumarate or caffeate. Phenolic acids were released by reUmChlE from natural substrates, such as destarched wheat bran, sugar beet pectin and coffee pulp. Treatment of wheat dough using reUmChlE resulted in a noticeable softening indicating a potential application of the enzyme in bakery and confectionery. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Chlorogenic Acid Esterase with a Unique Substrate Specificity from Ustilago maydis

PubMed Central

Haase-Aschoff, Paul; Kelle, Sebastian; Linke, Diana; Krings, Ulrich; Popper, Lutz; Berger, Ralf G.

2014-01-01

An extracellular chlorogenic acid esterase from Ustilago maydis (UmChlE) was purified to homogeneity by using three separation steps, including anion-exchange chromatography on a Q Sepharose FF column, preparative isoelectric focusing (IEF), and, finally, a combination of affinity chromatography and hydrophobic interaction chromatography on polyamide. SDS-PAGE analysis suggested a monomeric protein of ∼71 kDa. The purified enzyme showed maximal activity at pH 7.5 and at 37°C and was active over a wide pH range (3.5 to 9.5). Previously described chlorogenic acid esterases exhibited a comparable affinity for chlorogenic acid, but the enzyme from Ustilago was also active on typical feruloyl esterase substrates. Kinetic constants for chlorogenic acid, methyl p-coumarate, methyl caffeate, and methyl ferulate were as follows: Km values of 19.6 μM, 64.1 μM, 72.5 μM, and 101.8 μM, respectively, and kcat/Km values of 25.83 mM−1 s−1, 7.63 mM−1 s−1, 3.83 mM−1 s−1 and 3.75 mM−1 s−1, respectively. UmChlE released ferulic, p-coumaric, and caffeic acids from natural substrates such as destarched wheat bran (DSWB) and coffee pulp (CP), confirming activity on complex plant biomass. The full-length gene encoding UmChlE consisted of 1,758 bp, corresponding to a protein of 585 amino acids, and was functionally produced in Pichia pastoris GS115. Sequence alignments with annotated chlorogenic acid and feruloyl esterases underlined the uniqueness of this enzyme. PMID:25548041

KP4 to control Ustilago tritici in wheat: Enhanced greenhouse resistance to loose smut and changes in transcript abundance of pathogen related genes in infected KP4 plants.

PubMed

Quijano, Carolina Diaz; Wichmann, Fabienne; Schlaich, Thomas; Fammartino, Alessandro; Huckauf, Jana; Schmidt, Kerstin; Unger, Christoph; Broer, Inge; Sautter, Christof

2016-09-01

Ustilago tritici causes loose smut, which is a seed-borne fungal disease of wheat, and responsible for yield losses up to 40%. Loose smut is a threat to seed production in developing countries where small scale farmers use their own harvest as seed material. The killer protein 4 (KP4) is a virally encoded toxin from Ustilago maydis and inhibits growth of susceptible races of fungi from the Ustilaginales. Enhanced resistance in KP4 wheat to stinking smut, which is caused by Tilletia caries, had been reported earlier. We show that KP4 in genetically engineered wheat increased resistance to loose smut up to 60% compared to the non-KP4 control under greenhouse conditions. This enhanced resistance is dose and race dependent. The overexpression of the transgene kp4 and its effect on fungal growth have indirect effects on the expression of endogenous pathogen defense genes.

The 'PhenoBox', a flexible, automated, open-source plant phenotyping solution.

PubMed

Czedik-Eysenberg, Angelika; Seitner, Sebastian; Güldener, Ulrich; Koemeda, Stefanie; Jez, Jakub; Colombini, Martin; Djamei, Armin

2018-04-05

There is a need for flexible and affordable plant phenotyping solutions for basic research and plant breeding. We demonstrate our open source plant imaging and processing solution ('PhenoBox'/'PhenoPipe') and provide construction plans, source code and documentation to rebuild the system. Use of the PhenoBox is exemplified by studying infection of the model grass Brachypodium distachyon by the head smut fungus Ustilago bromivora, comparing phenotypic responses of maize to infection with a solopathogenic Ustilago maydis (corn smut) strain and effector deletion strains, and studying salt stress response in Nicotiana benthamiana. In U. bromivora-infected grass, phenotypic differences between infected and uninfected plants were detectable weeks before qualitative head smut symptoms. Based on this, we could predict the infection outcome for individual plants with high accuracy. Using a PhenoPipe module for calculation of multi-dimensional distances from phenotyping data, we observe a time after infection-dependent impact of U. maydis effector deletion strains on phenotypic response in maize. The PhenoBox/PhenoPipe system is able to detect established salt stress responses in N. benthamiana. We have developed an affordable, automated, open source imaging and data processing solution that can be adapted to various phenotyping applications in plant biology and beyond. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

A chlorogenic acid esterase with a unique substrate specificity from Ustilago maydis.

PubMed

Nieter, Annabel; Haase-Aschoff, Paul; Kelle, Sebastian; Linke, Diana; Krings, Ulrich; Popper, Lutz; Berger, Ralf G

2015-03-01

An extracellular chlorogenic acid esterase from Ustilago maydis (UmChlE) was purified to homogeneity by using three separation steps, including anion-exchange chromatography on a Q Sepharose FF column, preparative isoelectric focusing (IEF), and, finally, a combination of affinity chromatography and hydrophobic interaction chromatography on polyamide. SDS-PAGE analysis suggested a monomeric protein of ∼71 kDa. The purified enzyme showed maximal activity at pH 7.5 and at 37°C and was active over a wide pH range (3.5 to 9.5). Previously described chlorogenic acid esterases exhibited a comparable affinity for chlorogenic acid, but the enzyme from Ustilago was also active on typical feruloyl esterase substrates. Kinetic constants for chlorogenic acid, methyl p-coumarate, methyl caffeate, and methyl ferulate were as follows: Km values of 19.6 μM, 64.1 μM, 72.5 μM, and 101.8 μM, respectively, and kcat/Km values of 25.83 mM(-1) s(-1), 7.63 mM(-1) s(-1), 3.83 mM(-1) s(-1) and 3.75 mM(-1) s(-1), respectively. UmChlE released ferulic, p-coumaric, and caffeic acids from natural substrates such as destarched wheat bran (DSWB) and coffee pulp (CP), confirming activity on complex plant biomass. The full-length gene encoding UmChlE consisted of 1,758 bp, corresponding to a protein of 585 amino acids, and was functionally produced in Pichia pastoris GS115. Sequence alignments with annotated chlorogenic acid and feruloyl esterases underlined the uniqueness of this enzyme. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

The SPF27 Homologue Num1 Connects Splicing and Kinesin 1-Dependent Cytoplasmic Trafficking in Ustilago maydis

PubMed Central

Kellner, Nikola; Heimel, Kai; Obhof, Theresa; Finkernagel, Florian; Kämper, Jörg

2014-01-01

The conserved NineTeen protein complex (NTC) is an integral subunit of the spliceosome and required for intron removal during pre-mRNA splicing. The complex associates with the spliceosome and participates in the regulation of conformational changes of core spliceosomal components, stabilizing RNA-RNA- as well as RNA-protein interactions. In addition, the NTC is involved in cell cycle checkpoint control, response to DNA damage, as well as formation and export of mRNP-particles. We have identified the Num1 protein as the homologue of SPF27, one of NTC core components, in the basidiomycetous fungus Ustilago maydis. Num1 is required for polarized growth of the fungal hyphae, and, in line with the described NTC functions, the num1 mutation affects the cell cycle and cell division. The num1 deletion influences splicing in U. maydis on a global scale, as RNA-Seq analysis revealed increased intron retention rates. Surprisingly, we identified in a screen for Num1 interacting proteins not only NTC core components as Prp19 and Cef1, but several proteins with putative functions during vesicle-mediated transport processes. Among others, Num1 interacts with the motor protein Kin1 in the cytoplasm. Similar phenotypes with respect to filamentous and polar growth, vacuolar morphology, as well as the motility of early endosomes corroborate the genetic interaction between Num1 and Kin1. Our data implicate a previously unidentified connection between a component of the splicing machinery and cytoplasmic transport processes. As the num1 deletion also affects cytoplasmic mRNA transport, the protein may constitute a novel functional interconnection between the two disparate processes of splicing and trafficking. PMID:24391515

A Maize Cystatin Suppresses Host Immunity by Inhibiting Apoplastic Cysteine Proteases[C][W

PubMed Central

van der Linde, Karina; Hemetsberger, Christoph; Kastner, Christine; Kaschani, Farnusch; van der Hoorn, Renier A.L.; Kumlehn, Jochen; Doehlemann, Gunther

2012-01-01

Ustilago maydis is a biotrophic pathogen causing maize (Zea mays) smut disease. Transcriptome profiling of infected maize plants indicated that a gene encoding a putative cystatin (CC9) is induced upon penetration by U. maydis wild type. By contrast, cc9 is not induced after infection with the U. maydis effector mutant Δpep1, which elicits massive plant defenses. Silencing of cc9 resulted in a strongly induced maize defense gene expression and a hypersensitive response to U. maydis wild-type infection. Consequently, fungal colonization was strongly reduced in cc9-silenced plants, while recombinant CC9 prevented salicylic acid (SA)–induced defenses. Protease activity profiling revealed a strong induction of maize Cys proteases in SA-treated leaves, which could be inhibited by addition of CC9. Transgenic maize plants overexpressing cc9-mCherry showed an apoplastic localization of CC9. The transgenic plants showed a block in Cys protease activity and SA-dependent gene expression. Moreover, activated apoplastic Cys proteases induced SA-associated defense gene expression in naïve plants, which could be suppressed by CC9. We show that apoplastic Cys proteases play a pivotal role in maize defense signaling. Moreover, we identified cystatin CC9 as a novel compatibility factor that suppresses Cys protease activity to allow biotrophic interaction of maize with the fungal pathogen U. maydis. PMID:22454455

Activating Intrinsic Carbohydrate-Active Enzymes of the Smut Fungus Ustilago maydis for the Degradation of Plant Cell Wall Components

PubMed Central

Geiser, Elena; Reindl, Michèle; Blank, Lars M.; Feldbrügge, Michael

2016-01-01

ABSTRACT The microbial conversion of plant biomass to valuable products in a consolidated bioprocess could greatly increase the ecologic and economic impact of a biorefinery. Current strategies for hydrolyzing plant material mostly rely on the external application of carbohydrate-active enzymes (CAZymes). Alternatively, production organisms can be engineered to secrete CAZymes to reduce the reliance on externally added enzymes. Plant-pathogenic fungi have a vast repertoire of hydrolytic enzymes to sustain their lifestyle, but expression of the corresponding genes is usually highly regulated and restricted to the pathogenic phase. Here, we present a new strategy in using the biotrophic smut fungus Ustilago maydis for the degradation of plant cell wall components by activating its intrinsic enzyme potential during axenic growth. This fungal model organism is fully equipped with hydrolytic enzymes, and moreover, it naturally produces value-added substances, such as organic acids and biosurfactants. To achieve the deregulated expression of hydrolytic enzymes during the industrially relevant yeast-like growth in axenic culture, the native promoters of the respective genes were replaced by constitutively active synthetic promoters. This led to an enhanced conversion of xylan, cellobiose, and carboxymethyl cellulose to fermentable sugars. Moreover, a combination of strains with activated endoglucanase and β-glucanase increased the release of glucose from carboxymethyl cellulose and regenerated amorphous cellulose, suggesting that mixed cultivations could be a means for degrading more complex substrates in the future. In summary, this proof of principle demonstrates the potential applicability of activating the expression of native CAZymes from phytopathogens in a biocatalytic process. IMPORTANCE This study describes basic experiments that aim at the degradation of plant cell wall components by the smut fungus Ustilago maydis. As a plant pathogen, this fungus contains a set of lignocellulose-degrading enzymes that may be suited for biomass degradation. However, its hydrolytic enzymes are specifically expressed only during plant infection. Here, we provide the proof of principle that these intrinsic enzymes can be synthetically activated during the industrially relevant yeast-like growth. The fungus is known to naturally synthesize valuable compounds, such as itaconate or glycolipids. Therefore, it could be suited for use in a consolidated bioprocess in which more complex and natural substrates are simultaneously converted to fermentable sugars and to value-added compounds in the future. PMID:27316952

The mitochondrial alternative oxidase Aox1 is needed to cope with respiratory stress but dispensable for pathogenic development in Ustilago maydis

PubMed Central

Piñón-Zárate, Gabriela; Matus-Ortega, Genaro; Guerra, Guadalupe; Feldbrügge, Michael; Pardo, Juan Pablo

2017-01-01

The mitochondrial alternative oxidase is an important enzyme that allows respiratory activity and the functioning of the Krebs cycle upon disturbance of the respiration chain. It works as a security valve in transferring excessive electrons to oxygen, thereby preventing potential damage by the generation of harmful radicals. A clear biological function, besides the stress response, has so far convincingly only been shown for plants that use the alternative oxidase to generate heat to distribute volatiles. In fungi it was described that the alternative oxidase is needed for pathogenicity. Here, we investigate expression and function of the alternative oxidase at different stages of the life cycle of the corn pathogen Ustilago maydis (Aox1). Interestingly, expression of Aox1 is specifically induced during the stationary phase suggesting a role at high cell density when nutrients become limiting. Studying deletion strains as well as overexpressing strains revealed that Aox1 is dispensable for normal growth, for cell morphology, for response to temperature stress as well as for filamentous growth and plant pathogenicity. However, during conditions eliciting respiratory stress yeast-like growth as well as hyphal growth is strongly affected. We conclude that Aox1 is dispensable for the normal biology of the fungus but specifically needed to cope with respiratory stress. PMID:28273139

Role of the nuclear migration protein Lis1 in cell morphogenesis in Ustilago maydis

PubMed Central

Valinluck, Michael; Ahlgren, Sara; Sawada, Mizuho; Locken, Kristopher; Banuett, Flora

2010-01-01

Ustilago maydis is a basidiomycete fungus that exhibits a yeast-like and a filamentous form. Growth of the fungus in the host leads to additional morphological transitions. The different morphologies are characterized by distinct nuclear movements. Dynein and α-tubulin are required for nuclear movements and for cell morphogenesis of the yeast-like form. Lis1 is a microtubule plus-end tracking protein (+TIPs) conserved in eukaryotes and required for nuclear migration and spindle positioning. Defects in nuclear migration result in altered cell fate and aberrant development in metazoans, slow growth in fungi and disease in humans (e.g. lissencephaly). Here we investigate the role of the human LIS1 homolog in U. maydis and demonstrate that it is essential for cell viability, not previously seen in other fungi. With a conditional null mutation we show that lis1 is necessary for nuclear migration in the yeast-like cell and during the dimorphic transition. Studies of asynchronous exponentially growing cells and time-lapse microscopy uncovered novel functions of lis1: It is necessary for cell morphogenesis, positioning of the septum and cell wall integrity. lis1-depleted cells exhibit altered axes of growth and loss of cell polarity leading to grossly aberrant cells with clusters of nuclei and morphologically altered buds devoid of nuclei. Altered septum positioning and cell wall deposition contribute to the aberrant morphology. lis1-depleted cells lyse, indicative of altered cell wall properties or composition. We also demonstrate, with indirect immunofluorescence to visualize tubulin, that lis1 is necessary for the normal organization of the microtubule cytoskeleton: lis1-depleted cells contain more and longer microtubules that can form coils perpendicular to the long axis of the cell. We propose that lis1 controls microtubule dynamics and thus the regulated delivery of vesicles to growth sites and other cell domains that govern nuclear movements. PMID:20524583

Usefulness of heterologous promoters in the Pseudozyma flocculosa gene expression system.

PubMed

Avis, Tyler J; Anguenot, Raphaël; Neveu, Bertrand; Bolduc, Sébastien; Zhao, Yingyi; Cheng, Yali; Labbé, Caroline; Belzile, François; Bélanger, Richard R

2008-02-01

The basidiomycetous fungus Pseudozyma flocculosa represents a promising new host for the expression of complex recombinant proteins. Two novel heterologous promoter sequences, the Ustilago maydis glyceraldehyde-3-phosphate dehydrogenase (GPD) and Pseudozyma tsukubaensis alpha-glucosidase promoters, were tested for their ability to provide expression in P. flocculosa. In liquid medium, these two promoters produced lower levels of intracellular green fluorescent protein (GFP) as compared to the U. maydis hsp70 promoter. However, GPD and alpha-glucosidase sequences behaved as constitutive promoters whereas the hsp70 promoter appeared to be morphology-dependent. When using the hsp70 promoter, the expression of GFP increased proportionally to the concentration of hygromycin in the culture medium, indicating possible induction of the promoter by the antibiotic. Optimal solid-state culture conditions were designed for high throughput screening of hygromycin-resistant transformants with the hsp70 promoter in P. flocculosa.

Genetic analysis of biosurfactant production in Ustilago maydis.

PubMed

Hewald, Sandra; Josephs, Katharina; Bölker, Michael

2005-06-01

The dimorphic basidiomycete Ustilago maydis produces large amounts of surface-active compounds under conditions of nitrogen starvation. These biosurfactants consist of derivatives of two classes of amphipathic glycolipids. Ustilagic acids are cellobiose lipids in which the disaccharide is O-glycosidically linked to 15,16-dihydroxyhexadecanoic acid. Ustilipids are mannosylerythritol lipids derived from acylated beta-d-mannopyranosyl-d-erythritol. Whereas the chemical structure of these biosurfactants has been determined, the genetic basis for their biosynthesis and regulation is largely unknown. Here we report the first identification of two genes, emt1 and cyp1, that are essential for the production of fungal extracellular glycolipids. emt1 is required for mannosylerythritol lipid production and codes for a protein with similarity to prokaryotic glycosyltransferases involved in the biosynthesis of macrolide antibiotics. We suggest that Emt1 catalyzes the synthesis of mannosyl-d-erythritol by transfer of GDP-mannose. Deletion of the gene cyp1 resulted in complete loss of ustilagic acid production. Cyp1 encodes a cytochrome P450 monooxygenase which is highly related to a family of plant fatty acid hydroxylases. Therefore we assume that Cyp1 is directly involved in the biosynthesis of the unusual 15,16-dihydroxyhexadecanoic acid. We could show that mannosylerythritol lipid production is responsible for hemolytic activity on blood agar, whereas ustilagic acid secretion is required for long-range pheromone recognition. The mutants described here allow for the first time a genetic analysis of glycolipid production in fungi.

Genetic Analysis of Biosurfactant Production in Ustilago maydis

PubMed Central

Hewald, Sandra; Josephs, Katharina; Bölker, Michael

2005-01-01

The dimorphic basidiomycete Ustilago maydis produces large amounts of surface-active compounds under conditions of nitrogen starvation. These biosurfactants consist of derivatives of two classes of amphipathic glycolipids. Ustilagic acids are cellobiose lipids in which the disaccharide is O-glycosidically linked to 15,16-dihydroxyhexadecanoic acid. Ustilipids are mannosylerythritol lipids derived from acylated β-d-mannopyranosyl-d-erythritol. Whereas the chemical structure of these biosurfactants has been determined, the genetic basis for their biosynthesis and regulation is largely unknown. Here we report the first identification of two genes, emt1 and cyp1, that are essential for the production of fungal extracellular glycolipids. emt1 is required for mannosylerythritol lipid production and codes for a protein with similarity to prokaryotic glycosyltransferases involved in the biosynthesis of macrolide antibiotics. We suggest that Emt1 catalyzes the synthesis of mannosyl-d-erythritol by transfer of GDP-mannose. Deletion of the gene cyp1 resulted in complete loss of ustilagic acid production. Cyp1 encodes a cytochrome P450 monooxygenase which is highly related to a family of plant fatty acid hydroxylases. Therefore we assume that Cyp1 is directly involved in the biosynthesis of the unusual 15,16-dihydroxyhexadecanoic acid. We could show that mannosylerythritol lipid production is responsible for hemolytic activity on blood agar, whereas ustilagic acid secretion is required for long-range pheromone recognition. The mutants described here allow for the first time a genetic analysis of glycolipid production in fungi. PMID:15932999

The Ustilago maydis a2 Mating-Type Locus Genes lga2 and rga2 Compromise Pathogenicity in the Absence of the Mitochondrial p32 Family Protein Mrb1

PubMed Central

Bortfeld, Miriam; Auffarth, Kathrin; Kahmann, Regine; Basse, Christoph W.

2004-01-01

The Ustilago maydis mrb1 gene specifies a mitochondrial matrix protein with significant similarity to mitochondrial p32 family proteins known from human and many other eukaryotic species. Compatible mrb1 mutant strains were able to mate and form dikaryotic hyphae; however, proliferation within infected tissue and the ability to induce tumor development of infected maize (Zea mays) plants were drastically impaired. Surprisingly, manifestation of the mrb1 mutant phenotype selectively depended on the a2 mating type locus. The a2 locus contains, in addition to pheromone signaling components, the genes lga2 and rga2 of unknown function. Deletion of lga2 in an a2Δmrb1 strain fully restored pathogenicity, whereas pathogenicity was partially regained in an a2Δmrb1Δrga2 strain, implicating a concerted action between Lga2 and Rga2 in compromising pathogenicity in Δmrb1 strains. Lga2 and Rga2 localized to mitochondria and Mrb1 interacted with Rga2 in the yeast two-hybrid system. Conditional expression of lga2 in haploid cells reduced vegetative growth, conferred mitochondrial fragmentation and mitochondrial DNA degradation, and interfered with respiratory activity. The consequences of lga2 overexpression depended on the expression strength and were greatly exacerbated in Δmrb1 mutants. We propose that Lga2 interferes with mitochondrial fusion and that Mrb1 controls this activity, emphasizing a critical link between mitochondrial morphology and pathogenicity. PMID:15273296

Loss of virulence in Ustilago maydis by Umchs6 gene disruption.

PubMed

Garcerá-Teruel, Ana; Xoconostle-Cázares, Beatriz; Rosas-Quijano, Raymundo; Ortiz, Lucila; León-Ramírez, Claudia; Specht, Charles A; Sentandreu, Rafael; Ruiz-Herrera, José

2004-03-01

A gene encoding a sixth chitin synthase (Umchs6, sequence GenBank accession No. ) from the plant pathogenic hemibasidiomycete Ustilago maydis (DC.) Cda. was isolated and characterized. The predicted protein is 1103 amino acids in length with a calculated molecular mass of 123.5 kDa. a2b2 null mutants were obtained by substitution of a central fragment of the Umchs6 gene with the hygromycin resistance cassette, and a1b1 null mutants were obtained by genetic recombination in plants of an a2b2deltach6 and a wild-type a1b1 strain. The mutation had no effect on the dimorphic transition in vitro or on mating, and growth rate of the mutants was only slightly reduced. On the other hand, they displayed important alterations in cell morphology, particularly at the mycelial stage, and in the staining pattern with calcofluor white. Levels of chitin synthase activity in vitro and chitin content were reduced. The most noticeable characteristic of the mutants was their almost complete loss of virulence to maize (Zea mays L.). This was a recessive character. Microscopic observations during the infectious process suggest that chitin synthase 6 activity is very important for growth of the fungus into the plant. Transformation of a2b2deltach6 mutants with an autonomous replicating plasmid carrying the full Umchs6 gene restored their normal morphological phenotype and virulence. These results are evidence that the mutation in the Umchs6 gene was solely responsible for the phenotypic alterations observed.

Linkage of mating-type loci distinguishes bipolar from tetrapolar mating in basidiomycetous smut fungi.

PubMed Central

Bakkeren, G; Kronstad, J W

1994-01-01

Sexual compatibility requires self vs. non-self recognition. Genetically, two compatibility or mating-type systems govern recognition in heterothallic basidiomycete fungi such as the edible and woodrotting mushrooms and the economically important rust and smut phytopathogens. A bipolar system is defined by a single genetic locus (MAT) that can have two or multiple alleles. A tetrapolar system has two loci, each with two or more specificities. We have employed two species from the genus Ustilago (smut fungi) to discover a molecular explanation for the genetic difference in mating systems. Ustilago maydis, a tetrapolar species, has two genetically unlinked loci that encode the distinct mating functions of cell fusion (a locus) and subsequent sexual development and pathogenicity (b locus). We have recently described a b locus in a bipolar species, Ustilago hordei, wherein the existence of an a locus has been suspected, but not demonstrated. We report here the cloning of an allele of the a locus (a1) from U. hordei and the discovery that physical linkage of the a and b loci in this bipolar fungus accounts for the distinct mating system. Linkage establishes a large complex MAT locus in U. hordei; this locus appears to be in a region suppressed for recombination. Images PMID:7913746

Septation of infectious hyphae is critical for appressoria formation and virulence in the smut fungus Ustilago maydis.

PubMed

Freitag, Johannes; Lanver, Daniel; Böhmer, Christian; Schink, Kay Oliver; Bölker, Michael; Sandrock, Björn

2011-05-01

Differentiation of hyphae into specialized infection structures, known as appressoria, is a common feature of plant pathogenic fungi that penetrate the plant cuticle. Appressorium formation in U. maydis is triggered by environmental signals but the molecular mechanism of this hyphal differentiation is largely unknown. Infectious hyphae grow on the leaf surface by inserting regularly spaced retraction septa at the distal end of the tip cell leaving empty sections of collapsed hyphae behind. Here we show that formation of retraction septa is critical for appressorium formation and virulence in U. maydis. We demonstrate that the diaphanous-related formin Drf1 is necessary for actomyosin ring formation during septation of infectious hyphae. Drf1 acts as an effector of a Cdc42 GTPase signaling module, which also consists of the Cdc42-specific guanine nucleotide exchange factor Don1 and the Ste20-like kinase Don3. Deletion of drf1, don1 or don3 abolished formation of retraction septa resulting in reduced virulence. Appressorium formation in these mutants was not completely blocked but infection structures were found only at the tip of short filaments indicating that retraction septa are necessary for appressorium formation in extended infectious hyphae. In addition, appressoria of drf1 mutants penetrated the plant tissue less frequently.

Chemical genetics - a versatile method to combine science and higher level teaching in molecular genetics.

PubMed

Sandrock, Björn

2012-10-09

Phosphorylation is a key event in many cellular processes like cell cycle, transformation of environmental signals to transcriptional activation or polar growth. The chemical genetics approach can be used to analyse the effect of highly specific inhibition in vivo and is a promising method to screen for kinase targets. We have used this approach to study the role of the germinal centre kinase Don3 during the cell division in the phytopathogenic fungus Ustilago maydis. Due to the easy determination of the don3 phenotype we have chosen this approach for a genetic course for M.Sc. students and for IMPRS (International Max-Planck research school) students. According to the principle of "problem-based learning" the aim of this two-week course is to transfer knowledge about the broad spectrum of kinases to the students and that the students acquire the ability to design their own analog-sensitive kinase of interest. In addition to these training goals, we benefit from these annual courses the synthesis of basic constructs for genetic modification of several kinases in our model system U. maydis.

Establishing an unusual cell type: How to make a dikaryon

PubMed Central

Kruzel, Emilia K.; Hull, Christina M.

2010-01-01

Summary The dikaryons of basidiomycete fungi represent an unusual cell type required for complete sexual development. Dikaryon formation occurs via the activities of cell type-specific homeodomain transcription factors, which form regulatory complexes to establish the dikaryotic state. Decades of classical genetic and cell biological studies in mushrooms have provided a foundation for more recent molecular studies in the pathogenic species Ustilago maydis and Cryptococcus neoformans. Studies in these systems have revealed novel mechanisms of regulation that function downstream of classic homeodomain complexes to ensure that dikaryons are established and propagated. Comparisons of these dikaryon-specific networks promise to reveal the nature of regulatory network evolution and the adaptations responsible for driving complex eukaryotic development. PMID:21036099

Itaconic acid production in microorganisms.

PubMed

Zhao, Meilin; Lu, Xinyao; Zong, Hong; Li, Jinyang; Zhuge, Bin

2018-03-01

Itaconic acid, 2-methylidenebutanedioic acid, is a precursor of polymers, chemicals, and fuels. Many fungi can synthesize itaconic acid; Aspergillus terreus and Ustilago maydis produce up to 85 and 53 g l -1 , respectively. Other organisms, including Aspergillus niger and yeasts, have been engineered to produce itaconic acid. However, the titer of itaconic acid is low compared with the analogous major fermentation product, citric acid, for which the yield is > 200 g l -1 . Here, we review two types of pathway for itaconic acid biosynthesis as well as recent advances by metabolic engineering strategies and process optimization to enhance itaconic acid productivity in native producers and heterologous hosts. We also propose further improvements to overcome existing problems.

An assay for entry of secreted fungal effectors into plant cells.

PubMed

Lo Presti, Libera; Zechmann, Bernd; Kumlehn, Jochen; Liang, Liang; Lanver, Daniel; Tanaka, Shigeyuki; Bock, Ralph; Kahmann, Regine

2017-01-01

Successful colonization of plants by prokaryotic and eukaryotic pathogens requires active effector-mediated suppression of defense responses and host tissue reprogramming. Secreted effector proteins can either display their activity in the apoplast or translocate into host cells and function therein. Although characterized in bacteria, the molecular mechanisms of effector delivery by fungal phytopathogens remain elusive. Here we report the establishment of an assay that is based on biotinylation of effectors in the host cytoplasm as hallmark of uptake. The assay exploits the ability of the bacterial biotin ligase BirA to biotinylate any protein that carries a short peptide (Avitag). It is based on the stable expression of BirA in the cytoplasm of maize plants and on engineering of Ustilago maydis strains to secrete Avitagged effectors. We demonstrate translocation of a number of effectors in the U. maydis-maize system and show data that suggest that the uptake mechanism could be rather nonspecific The assay promises to be a powerful tool for the classification of effectors as well as for the functional study of effector uptake mechanism not only in the chosen system but more generally for systems where biotrophic interactions are established. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Living and Thriving on the Skin: Malassezia Genomes Tell the Story

PubMed Central

Coelho, Marco A.; Sampaio, José Paulo; Gonçalves, Paula

2013-01-01

ABSTRACT Our understanding of the interactions between normal skin microbiota and the human host has been greatly extended by recent investigations. In their recent study in mBio, A. Gioti et al. (mBio 4[1]:e00572-12, 2013) sequenced the genome of the atopic eczema-associated yeast, Malassezia sympodialis, and compared its gene content and organization with that of Malassezia globosa, a species implicated in dandruff. Their findings were also contrasted with those previously obtained for Ustilago maydis, which is a close relative but ecologically distinct plant parasite. Besides gaining additional insight into key host-specific adaptations and the particular function and molecular evolution of allergens related to atopic eczema, Gioti et al. also uncovered several lines of evidence that elegantly suggest the presence of an extant sexual cycle, with important implications in disease. PMID:23512963

Fungal model systems and the elucidation of pathogenicity determinants

PubMed Central

Perez-Nadales, Elena; Almeida Nogueira, Maria Filomena; Baldin, Clara; Castanheira, Sónia; El Ghalid, Mennat; Grund, Elisabeth; Lengeler, Klaus; Marchegiani, Elisabetta; Mehrotra, Pankaj Vinod; Moretti, Marino; Naik, Vikram; Oses-Ruiz, Miriam; Oskarsson, Therese; Schäfer, Katja; Wasserstrom, Lisa; Brakhage, Axel A.; Gow, Neil A.R.; Kahmann, Regine; Lebrun, Marc-Henri; Perez-Martin, José; Di Pietro, Antonio; Talbot, Nicholas J.; Toquin, Valerie; Walther, Andrea; Wendland, Jürgen

2014-01-01

Fungi have the capacity to cause devastating diseases of both plants and animals, causing significant harvest losses that threaten food security and human mycoses with high mortality rates. As a consequence, there is a critical need to promote development of new antifungal drugs, which requires a comprehensive molecular knowledge of fungal pathogenesis. In this review, we critically evaluate current knowledge of seven fungal organisms used as major research models for fungal pathogenesis. These include pathogens of both animals and plants; Ashbya gossypii, Aspergillus fumigatus, Candida albicans, Fusarium oxysporum, Magnaporthe oryzae, Ustilago maydis and Zymoseptoria tritici. We present key insights into the virulence mechanisms deployed by each species and a comparative overview of key insights obtained from genomic analysis. We then consider current trends and future challenges associated with the study of fungal pathogenicity. PMID:25011008

The Corn Smut ('Huitlacoche') as a New Platform for Oral Vaccines.

PubMed

Juárez-Montiel, Margarita; Romero-Maldonado, Andrea; Monreal-Escalante, Elizabeth; Becerra-Flora, Alicia; Korban, Schuyler S; Rosales-Mendoza, Sergio; Jiménez-Bremont, Juan Francisco

2015-01-01

The development of new alternative platforms for subunit vaccine production is a priority in the biomedical field. In this study, Ustilago maydis, the causal agent of common corn smut or 'huitlacoche'has been genetically engineered to assess expression and immunogenicity of the B subunit of the cholera toxin (CTB), a relevant immunomodulatory agent in vaccinology. An oligomeric CTB recombinant protein was expressed in corn smut galls at levels of up to 1.3 mg g-1 dry weight (0.8% of the total soluble protein). Mice orally immunized with 'huitlacoche'-derived CTB showed significant humoral responses that were well-correlated with protection against challenge with the cholera toxin (CT). These findings demonstrate the feasibility of using edible corn smut as a safe, effective, and low-cost platform for production and delivery of a subunit oral vaccine. The implications of this platform in the area of molecular pharming are discussed.

Aberrant Synthesis of Indole-3-Acetic Acid in Saccharomyces cerevisiae Triggers Morphogenic Transition, a Virulence Trait of Pathogenic Fungi

PubMed Central

Rao, Reeta Prusty; Hunter, Ally; Kashpur, Olga; Normanly, Jennifer

2010-01-01

Many plant-associated microbes synthesize the auxin indole-3-acetic acid (IAA), and several IAA biosynthetic pathways have been identified in microbes and plants. Saccharomyces cerevisiae has previously been shown to respond to IAA by inducing pseudohyphal growth. We observed that IAA also induced hyphal growth in the human pathogen Candida albicans and thus may function as a secondary metabolite signal that regulates virulence traits such as hyphal transition in pathogenic fungi. Aldehyde dehydrogenase (Ald) is required for IAA synthesis from a tryptophan (Trp) precursor in Ustilago maydis. Mutant S. cerevisiae with deletions in two ALD genes are unable to convert radiolabeled Trp to IAA, yet produce IAA in the absence of exogenous Trp and at levels higher than wild type. These data suggest that yeast may have multiple pathways for IAA synthesis, one of which is not dependent on Trp. PMID:20233857

Genetic transformation of the plant pathogens Phytophthora capsici and Phytophthora parasitica.

PubMed Central

Bailey, A M; Mena, G L; Herrera-Estrella, L

1991-01-01

Phytophthora capsici and P.parasitica were transformed to hygromycin B resistance using plasmids pCM54 and pHL1, which contain the bacterial hygromycin B phosphotransferase gene (hph) fused to promoter elements of the Ustilago maydis heat shock hsp70 gene. Enzymes Driselase and Novozyme 234 were used to generate protoplasts which were then transformed following exposure to plasmid DNA and polyethylene glycol 6000. Transformation frequencies of over 500 transformants per micrograms of DNA per 1 x 10(6) protoplasts were obtained. Plasmid pCM54 appears to be transmitted in Phytophthora spp. as an extra-chromosomal element through replication, as shown by Southern blot hybridization and by the loss of plasmid methylation. In addition, transformed strains retained their capacity of infecting Serrano pepper seedlings and Mc. Intosh apple fruits, the host plants for P.capsici and P.parasitica, respectively. Images PMID:1651483

The Corn Smut (‘Huitlacoche’) as a New Platform for Oral Vaccines

PubMed Central

Juárez-Montiel, Margarita; Romero-Maldonado, Andrea; Monreal-Escalante, Elizabeth; Becerra-Flora, Alicia; Korban, Schuyler S.; Rosales-Mendoza, Sergio; Jiménez-Bremont, Juan Francisco

2015-01-01

The development of new alternative platforms for subunit vaccine production is a priority in the biomedical field. In this study, Ustilago maydis, the causal agent of common corn smut or ‘huitlacoche’has been genetically engineered to assess expression and immunogenicity of the B subunit of the cholera toxin (CTB), a relevant immunomodulatory agent in vaccinology. An oligomeric CTB recombinant protein was expressed in corn smut galls at levels of up to 1.3 mg g-1 dry weight (0.8% of the total soluble protein). Mice orally immunized with ‘huitlacoche’-derived CTB showed significant humoral responses that were well-correlated with protection against challenge with the cholera toxin (CT). These findings demonstrate the feasibility of using edible corn smut as a safe, effective, and low-cost platform for production and delivery of a subunit oral vaccine. The implications of this platform in the area of molecular pharming are discussed. PMID:26207365

Long-distance endosome trafficking drives fungal effector production during plant infection

PubMed Central

Bielska, Ewa; Higuchi, Yujiro; Schuster, Martin; Steinberg, Natascha; Kilaru, Sreedhar; Talbot, Nicholas J.; Steinberg, Gero

2014-01-01

To cause plant disease, pathogenic fungi can secrete effector proteins into plant cells to suppress plant immunity and facilitate fungal infection. Most fungal pathogens infect plants using very long strand-like cells, called hyphae, that secrete effectors from their tips into host tissue. How fungi undergo long-distance cell signalling to regulate effector production during infection is not known. Here we show that long-distance retrograde motility of early endosomes (EEs) is necessary to trigger transcription of effector-encoding genes during plant infection by the pathogenic fungus Ustilago maydis. We demonstrate that motor-dependent retrograde EE motility is necessary for regulation of effector production and secretion during host cell invasion. We further show that retrograde signalling involves the mitogen-activated kinase Crk1 that travels on EEs and participates in control of effector production. Fungal pathogens therefore undergo long-range signalling to orchestrate host invasion. PMID:25283249

Of smuts, blasts, mildews, and blights: cAMP signaling in phytopathogenic fungi.

PubMed

Lee, Nancy; D'Souza, Cletus A; Kronstad, James W

2003-01-01

cAMP regulates morphogenesis and virulence in a wide variety of fungi including the plant pathogens. In saprophytic yeasts such as Saccharomyces cerevisiae, cAMP signaling plays an important role in nutrient sensing. In filamentous saprophytes, the cAMP pathway appears to play an integral role in vegetative growth and sporulation, with possible connections to mating. Infection-related morphogenesis includes sporulation (conidia and teliospores), formation of appressoria, infection hyphae, and sclerotia. Here, we review studies of cAMP signaling in a variety of plant fungal pathogens. The primary fungi to be considered include Ustilago maydis, Magnaporthe grisea, Cryphonectria parasitica, Colletotrichum and Fusarium species, and Erisyphe graminis. We also include related information on Trichoderma species that act as mycoparasites and biocontrol agents of phytopathogenic fungi. We point out similarities in infection mechanisms, conservation of signaling components, as well as instances of cross-talk with other signaling pathways.

Long-distance endosome trafficking drives fungal effector production during plant infection.

PubMed

Bielska, Ewa; Higuchi, Yujiro; Schuster, Martin; Steinberg, Natascha; Kilaru, Sreedhar; Talbot, Nicholas J; Steinberg, Gero

2014-10-06

To cause plant disease, pathogenic fungi can secrete effector proteins into plant cells to suppress plant immunity and facilitate fungal infection. Most fungal pathogens infect plants using very long strand-like cells, called hyphae, that secrete effectors from their tips into host tissue. How fungi undergo long-distance cell signalling to regulate effector production during infection is not known. Here we show that long-distance retrograde motility of early endosomes (EEs) is necessary to trigger transcription of effector-encoding genes during plant infection by the pathogenic fungus Ustilago maydis. We demonstrate that motor-dependent retrograde EE motility is necessary for regulation of effector production and secretion during host cell invasion. We further show that retrograde signalling involves the mitogen-activated kinase Crk1 that travels on EEs and participates in control of effector production. Fungal pathogens therefore undergo long-range signalling to orchestrate host invasion.

A Gene Cluster for Biosynthesis of Mannosylerythritol Lipids Consisted of 4-O-β-D-Mannopyranosyl-(2R,3S)-Erythritol as the Sugar Moiety in a Basidiomycetous Yeast Pseudozyma tsukubaensis

PubMed Central

Saika, Azusa; Koike, Hideaki; Fukuoka, Tokuma; Yamamoto, Shuhei; Kishimoto, Takahide; Morita, Tomotake

2016-01-01

Mannosylerythritol lipids (MELs) belong to the glycolipid biosurfactants and are produced by various fungi. The basidiomycetous yeast Pseudozyma tsukubaensis produces diastereomer type of MEL-B, which contains 4-O-β-D-mannopyranosyl-(2R,3S)-erythritol (R-form) as the sugar moiety. In this respect it differs from conventional type of MELs, which contain 4-O-β-D-mannopyranosyl-(2S,3R)-erythritol (S-form) as the sugar moiety. While the biosynthetic gene cluster for conventional type of MELs has been previously identified in Ustilago maydis and Pseudozyma antarctica, the genetic basis for MEL biosynthesis in P. tsukubaensis is unknown. Here, we identified a gene cluster involved in MEL biosynthesis in P. tsukubaensis. Among these genes, PtEMT1, which encodes erythritol/mannose transferase, had greater than 69% identity with homologs from strains in the genera Ustilago, Melanopsichium, Sporisorium and Pseudozyma. However, phylogenetic analysis placed PtEMT1p in a separate clade from the other proteins. To investigate the function of PtEMT1, we introduced the gene into a P. antarctica mutant strain, ΔPaEMT1, which lacks MEL biosynthesis ability owing to the deletion of PaEMT1. Using NMR spectroscopy, we identified the biosynthetic product as MEL-A with altered sugar conformation. These results indicate that PtEMT1p catalyzes the sugar conformation of MELs. This is the first report of a gene cluster for the biosynthesis of diastereomer type of MEL. PMID:27327162

The ESCRT regulator Did2 maintains the balance between long-distance endosomal transport and endocytic trafficking

PubMed Central

Haag, Carl

2017-01-01

In highly polarised cells, like fungal hyphae, early endosomes function in both endocytosis as well as long-distance transport of various cargo including mRNA and protein complexes. However, knowledge on the crosstalk between these seemingly different trafficking processes is scarce. Here, we demonstrate that the ESCRT regulator Did2 coordinates endosomal transport in fungal hyphae of Ustilago maydis. Loss of Did2 results in defective vacuolar targeting, less processive long-distance transport and abnormal shuttling of early endosomes. Importantly, the late endosomal protein Rab7 and vacuolar protease Prc1 exhibit increased shuttling on these aberrant endosomes suggesting defects in endosomal maturation and identity. Consistently, molecular motors fail to attach efficiently explaining the disturbed processive movement. Furthermore, the endosomal mRNP linker protein Upa1 is hardly present on endosomes resulting in defects in long-distance mRNA transport. In conclusion, the ESCRT regulator Did2 coordinates precise maturation of endosomes and thus provides the correct membrane identity for efficient endosomal long-distance transport. PMID:28422978

Active diffusion and microtubule-based transport oppose myosin forces to position organelles in cells

PubMed Central

Lin, Congping; Schuster, Martin; Guimaraes, Sofia Cunha; Ashwin, Peter; Schrader, Michael; Metz, Jeremy; Hacker, Christian; Gurr, Sarah Jane; Steinberg, Gero

2016-01-01

Even distribution of peroxisomes (POs) and lipid droplets (LDs) is critical to their role in lipid and reactive oxygen species homeostasis. How even distribution is achieved remains elusive, but diffusive motion and directed motility may play a role. Here we show that in the fungus Ustilago maydis ∼95% of POs and LDs undergo diffusive motions. These movements require ATP and involve bidirectional early endosome motility, indicating that microtubule-associated membrane trafficking enhances diffusion of organelles. When early endosome transport is abolished, POs and LDs drift slowly towards the growing cell end. This pole-ward drift is facilitated by anterograde delivery of secretory cargo to the cell tip by myosin-5. Modelling reveals that microtubule-based directed transport and active diffusion support distribution, mobility and mixing of POs. In mammalian COS-7 cells, microtubules and F-actin also counteract each other to distribute POs. This highlights the importance of opposing cytoskeletal forces in organelle positioning in eukaryotes. PMID:27251117

Protein profile and protein interaction network of Moniliophthora perniciosa basidiospores.

PubMed

Mares, Joise Hander; Gramacho, Karina Peres; Dos Santos, Everton Cruz; Santiago, André da Silva; Silva, Edson Mário de Andrade; Alvim, Fátima Cerqueira; Pirovani, Carlos Priminho

2016-06-24

Witches' broom, a disease caused by the basidiomycete Moniliophthora perniciosa, is considered to be the most important disease of the cocoa crop in Bahia, an area in the Brazilian Amazon, and also in the other countries where it is found. M. perniciosa germ tubes may penetrate into the host through intact or natural openings in the cuticle surface, in epidermis cell junctions, at the base of trichomes, or through the stomata. Despite its relevance to the fungal life cycle, basidiospore biology has not been extensively investigated. In this study, our goal was to optimize techniques for producing basidiospores for protein extraction, and to produce the first proteomics analysis map of ungerminated basidiospores. We then presented a protein interaction network by using Ustilago maydis as a model. The average pileus area ranged from 17.35 to 211.24 mm(2). The minimum and maximum productivity were 23,200 and 6,666,667 basidiospores per basidiome, respectively. The protein yield in micrograms per million basidiospores were approximately 0.161; 2.307, and 3.582 for germination times of 0, 2, and 4 h after germination, respectively. A total of 178 proteins were identified through mass spectrometry. These proteins were classified according to their molecular function and their involvement in biological processes such as cellular energy production, oxidative metabolism, stress, protein synthesis, and protein folding. Furthermore, to better understand the expression pattern, signaling, and interaction events of spore proteins, we presented an interaction network using orthologous proteins from Ustilago maydis as a model. Most of the orthologous proteins that were identified in this study were not clustered in the network, but several of them play a very important role in hypha development and branching. The quantities of basidiospores 7 × 10(9); 5.2 × 10(8), and 6.7 × 10(8) were sufficient to obtain enough protein mass for the three 2D-PAGE replicates, for the 0, 2, and 4 h-treatments, respectively. The protein extraction method that is based on sedimentation, followed by sonication with SDS-dense buffer, and phenolic extraction, which was utilized in this study, was effective, presenting a satisfactory resolution and reproducibility for M. perniciosa basidiospores. This report constitutes the first comprehensive study of protein expression during the ungerminated stage of the M. perniciosa basidiospore. Identification of the spots observed in the reference gel enabled us to know the main molecular interactions involved in the initial metabolic processes of fungal development.

In silico mapping of quantitative trait loci in maize.

PubMed

Parisseaux, B; Bernardo, R

2004-08-01

Quantitative trait loci (QTL) are most often detected through designed mapping experiments. An alternative approach is in silico mapping, whereby genes are detected using existing phenotypic and genomic databases. We explored the usefulness of in silico mapping via a mixed-model approach in maize (Zea mays L.). Specifically, our objective was to determine if the procedure gave results that were repeatable across populations. Multilocation data were obtained from the 1995-2002 hybrid testing program of Limagrain Genetics in Europe. Nine heterotic patterns comprised 22,774 single crosses. These single crosses were made from 1,266 inbreds that had data for 96 simple sequence repeat (SSR) markers. By a mixed-model approach, we estimated the general combining ability effects associated with marker alleles in each heterotic pattern. The numbers of marker loci with significant effects--37 for plant height, 24 for smut [Ustilago maydis (DC.) Cda.] resistance, and 44 for grain moisture--were consistent with previous results from designed mapping experiments. Each trait had many loci with small effects and few loci with large effects. For smut resistance, a marker in bin 8.05 on chromosome 8 had a significant effect in seven (out of a maximum of 18) instances. For this major QTL, the maximum effect of an allele substitution ranged from 5.4% to 41.9%, with an average of 22.0%. We conclude that in silico mapping via a mixed-model approach can detect associations that are repeatable across different populations. We speculate that in silico mapping will be more useful for gene discovery than for selection in plant breeding programs. Copyright 2004 Springer-Verlag

Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences.

PubMed

Padliya, Neerav D; Garrett, Wesley M; Campbell, Kimberly B; Tabb, David L; Cooper, Bret

2007-11-01

LC-MS/MS has demonstrated potential for detecting plant pathogens. Unlike PCR or ELISA, LC-MS/MS does not require pathogen-specific reagents for the detection of pathogen-specific proteins and peptides. However, the MS/MS approach we and others have explored does require a protein sequence reference database and database-search software to interpret tandem mass spectra. To evaluate the limitations of database composition on pathogen identification, we analyzed proteins from cultured Ustilago maydis, Phytophthora sojae, Fusarium graminearum, and Rhizoctonia solani by LC-MS/MS. When the search database did not contain sequences for a target pathogen, or contained sequences to related pathogens, target pathogen spectra were reliably matched to protein sequences from nontarget organisms, giving an illusion that proteins from nontarget organisms were identified. Our analysis demonstrates that when database-search software is used as part of the identification process, a paradox exists whereby additional sequences needed to detect a wide variety of possible organisms may lead to more cross-species protein matches and misidentification of pathogens.

Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers

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

Labbe, Jessy L; Murat, Claude; Morin, Emmanuelle

It is becoming clear that simple sequence repeats (SSRs) play a significant role in fungal genome organization, and they are a large source of genetic markers for population genetics and meiotic maps. We identified SSRs in the Laccaria bicolor genome by in silico survey and analyzed their distribution in the different genomic regions. We also compared the abundance and distribution of SSRs in L. bicolor with those of the following fungal genomes: Phanerochaete chrysosporium, Coprinopsis cinerea, Ustilago maydis, Cryptococcus neoformans, Aspergillus nidulans, Magnaporthe grisea, Neurospora crassa and Saccharomyces cerevisiae. Using the MISA computer program, we detected 277,062 SSRs in themore » L. bicolor genome representing 8% of the assembled genomic sequence. Among the analyzed basidiomycetes, L. bicolor exhibited the highest SSR density although no correlation between relative abundance and the genome sizes was observed. In most genomes the short motifs (mono- to trinucleotides) were more abundant than the longer repeated SSRs. Generally, in each organism, the occurrence, relative abundance, and relative density of SSRs decreased as the repeat unit increased. Furthermore, each organism had its own common and longest SSRs. In the L. bicolor genome, most of the SSRs were located in intergenic regions (73.3%) and the highest SSR density was observed in transposable elements (TEs; 6,706 SSRs/Mb). However, 81% of the protein-coding genes contained SSRs in their exons, suggesting that SSR polymorphism may alter gene phenotypes. Within a L. bicolor offspring, sequence polymorphism of 78 SSRs was mainly detected in non-TE intergenic regions. Unlike previously developed microsatellite markers, these new ones are spread throughout the genome; these markers could have immediate applications in population genetics.« less

Proposal to conserve the name Helminthosporium maydis Y. Nisik. & C. Miyake (Bipolaris maydis) against H. maydis Brond. and Ophiobolus heterostrophus (Ascomycota: Pleosporales: Pleosporaceae)

USDA-ARS?s Scientific Manuscript database

The name Bipolaris maydis (Y. Nisik. & C. Miyake) Shoemaker is the type of the genus Bipolaris Shoemaker, while Cochliobolus heterostrophus (Drechsler) Drechsler is the type of the genus Cochliobolus Drechsler. Initially described as Helminthosporium maydis Y. Nisik. & C. Miyake, Bipolaris maydis is...

Hook is an adapter that coordinates kinesin-3 and dynein cargo attachment on early endosomes

PubMed Central

Bielska, Ewa; Schuster, Martin; Roger, Yvonne; Berepiki, Adokiye; Soanes, Darren M.; Talbot, Nicholas J.

2014-01-01

Bidirectional membrane trafficking along microtubules is mediated by kinesin-1, kinesin-3, and dynein. Several organelle-bound adapters for kinesin-1 and dynein have been reported that orchestrate their opposing activity. However, the coordination of kinesin-3/dynein-mediated transport is not understood. In this paper, we report that a Hook protein, Hok1, is essential for kinesin-3– and dynein-dependent early endosome (EE) motility in the fungus Ustilago maydis. Hok1 binds to EEs via its C-terminal region, where it forms a complex with homologues of human fused toes (FTS) and its interactor FTS- and Hook-interacting protein. A highly conserved N-terminal region is required to bind dynein and kinesin-3 to EEs. To change the direction of EE transport, kinesin-3 is released from organelles, and dynein binds subsequently. A chimaera of human Hook3 and Hok1 rescues the hok1 mutant phenotype, suggesting functional conservation between humans and fungi. We conclude that Hok1 is part of an evolutionarily conserved protein complex that regulates bidirectional EE trafficking by controlling attachment of both kinesin-3 and dynein. PMID:24637326

A split motor domain in a cytoplasmic dynein

PubMed Central

Straube, Anne; Enard, Wolfgang; Berner, Alexandra; Wedlich-Söldner, Roland; Kahmann, Regine; Steinberg, Gero

2001-01-01

The heavy chain of dynein forms a globular motor domain that tightly couples the ATP-cleavage region and the microtubule-binding site to transform chemical energy into motion along the cytoskeleton. Here we show that, in the fungus Ustilago maydis, two genes, dyn1 and dyn2, encode the dynein heavy chain. The putative ATPase region is provided by dyn1, while dyn2 includes the predicted microtubule-binding site. Both genes are located on different chromosomes, are transcribed into independent mRNAs and are translated into separate polypeptides. Both Dyn1 and Dyn2 co-immunoprecipitated and co-localized within growing cells, and Dyn1–Dyn2 fusion proteins partially rescued mutant phenotypes, suggesting that both polypeptides interact to form a complex. In cell extracts the Dyn1–Dyn2 complex dissociated, and microtubule affinity purification indicated that Dyn1 or associated polypeptides bind microtubules independently of Dyn2. Both Dyn1 and Dyn2 were essential for cell survival, and conditional mutants revealed a common role in nuclear migration, cell morphogenesis and microtubule organization, indicating that the Dyn1–Dyn2 complex serves multiple cellular functions. PMID:11566874

The Plant-Dependent Life Cycle of Thecaphora thlaspeos: A Smut Fungus Adapted to Brassicaceae.

PubMed

Frantzeskakis, Lamprinos; Courville, Kaitlyn J; Plücker, Lesley; Kellner, Ronny; Kruse, Julia; Brachmann, Andreas; Feldbrügge, Michael; Göhre, Vera

2017-04-01

Smut fungi are globally distributed plant pathogens that infect agriculturally important crop plants such as maize or potato. To date, molecular studies on plant responses to smut fungi are challenging due to the genetic complexity of their host plants. Therefore, we set out to investigate the known smut fungus of Brassicaceae hosts, Thecaphora thlaspeos. T. thlaspeos infects different Brassicaceae plant species throughout Europe, including the perennial model plant Arabis alpina. In contrast to characterized smut fungi, mature and dry T. thlaspeos teliospores germinated only in the presence of a plant signal. An infectious filament emerges from the teliospore, which can proliferate as haploid filamentous cultures. Haploid filaments from opposite mating types mate, similar to sporidia of the model smut fungus Ustilago maydis. Consistently, the a and b mating locus genes are conserved. Infectious filaments can penetrate roots and aerial tissues of host plants, causing systemic colonization along the vasculature. Notably, we could show that T. thlaspeos also infects Arabidopsis thaliana. Exploiting the genetic resources of A. thaliana and Arabis alpina will allow us to characterize plant responses to smut infection in a comparative manner and, thereby, characterize factors for endophytic growth as well as smut fungi virulence in dicot plants.

Application of quasi-steady state methods to molecular motor transport on microtubules in fungal hyphae.

PubMed

Dauvergne, Duncan; Edelstein-Keshet, Leah

2015-08-21

We consider bidirectional transport of cargo by molecular motors dynein and kinesin that walk along microtubules, and/or diffuse in the cell. The motors compete to transport cargo in opposite directions with respect to microtubule polarity (towards the plus or minus end of the microtubule). In recent work, Gou et al. (2014) used a hierarchical set of models, each consisting of continuum transport equations to track the evolution of motors and their cargo (early endosomes) in the specific case of the fungus Ustilago maydis. We complement their work using a framework of quasi-steady state analysis developed by Newby and Bressloff (2010) and Bressloff and Newby (2013) to reduce the models to an approximating steady state Fokker-Plank equation. This analysis allows us to find analytic approximations to the steady state solutions in many cases where the full models are not easily solved. Consequently, we can make predictions about parameter dependence of the resulting spatial distributions. We also characterize the overall rates of bulk transport and diffusion, and how these are related to state transition parameters, motor speeds, microtubule polarity distribution, and specific assumptions made. Copyright © 2015 Elsevier Ltd. All rights reserved.

Principles of mRNA transport in yeast.

PubMed

Heym, Roland Gerhard; Niessing, Dierk

2012-06-01

mRNA localization and localized translation is a common mechanism by which cellular asymmetry is achieved. In higher eukaryotes the mRNA transport machinery is required for such diverse processes as stem cell division and neuronal plasticity. Because mRNA localization in metazoans is highly complex, studies at the molecular level have proven to be cumbersome. However, active mRNA transport has also been reported in fungi including Saccharomyces cerevisiae, Ustilago maydis and Candida albicans, in which these events are less difficult to study. Amongst them, budding yeast S. cerevisiae has yielded mechanistic insights that exceed our understanding of other mRNA localization events to date. In contrast to most reviews, we refrain here from summarizing mRNA localization events from different organisms. Instead we give an in-depth account of ASH1 mRNA localization in budding yeast. This approach is particularly suited to providing a more holistic view of the interconnection between the individual steps of mRNA localization, from transcriptional events to cytoplasmic mRNA transport and localized translation. Because of our advanced mechanistic understanding of mRNA localization in yeast, the present review may also be informative for scientists working, for example, on mRNA localization in embryogenesis or in neurons.

Comparative genomics of maize ear rot pathogens reveals expansion of carbohydrate-active enzymes and secondary metabolism backbone genes in Stenocarpella maydis.

PubMed

Zaccaron, Alex Z; Woloshuk, Charles P; Bluhm, Burton H

2017-11-01

Stenocarpella maydis is a plant pathogenic fungus that causes Diplodia ear rot, one of the most destructive diseases of maize. To date, little information is available regarding the molecular basis of pathogenesis in this organism, in part due to limited genomic resources. In this study, a 54.8 Mb draft genome assembly of S. maydis was obtained with Illumina and PacBio sequencing technologies, and analyzed. Comparative genomic analyses with the predominant maize ear rot pathogens Aspergillus flavus, Fusarium verticillioides, and Fusarium graminearum revealed an expanded set of carbohydrate-active enzymes for cellulose and hemicellulose degradation in S. maydis. Analyses of predicted genes involved in starch degradation revealed six putative α-amylases, four extracellular and two intracellular, and two putative γ-amylases, one of which appears to have been acquired from bacteria via horizontal transfer. Additionally, 87 backbone genes involved in secondary metabolism were identified, which represents one of the largest known assemblages among Pezizomycotina species. Numerous secondary metabolite gene clusters were identified, including two clusters likely involved in the biosynthesis of diplodiatoxin and chaetoglobosins. The draft genome of S. maydis presented here will serve as a useful resource for molecular genetics, functional genomics, and analyses of population diversity in this organism. Copyright © 2017 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Maize chiA as a Potential Genetic Marker for Stenocarpella maydis Ear Rot Resistance

USDA-ARS?s Scientific Manuscript database

Stenocarpella maydis (Diplodia maydis) is the most prevalent ear rot pathogen in nearly all countries where maize is produced. The genetic basis of plant resistance to S. maydis appears to rely on multiple genetic factors, none of which are known. We previously reported that S. maydis secretes a p...

Cephalosporium maydis is a distinct species in the Gaeumannomyces-Harpophora species complex.

PubMed

Saleh, Amgad A; Leslie, John F

2004-01-01

Cephalosporium maydis is an important plant pathogen whose phylogenetic position relative to other fungi has not been established clearly. We compared strains of C. maydis, strains from several other plant-pathogenic Cephalosporium spp. and several possible relatives within the Gaeumannomyces-Harpophora species complex, to which C. maydis has been suggested to belong based on previous preliminary DNA sequence analyses. DNA sequences of the nuclear genes encoding the rDNA ITS region, β-tubulin, histone H3, and MAT-2 support the hypothesis that C. maydis is a distinct taxon within the Gaeumannomyces-Harpophora species complex. Based on amplified fragment length polymorphism (AFLP) profiles, C. maydis also is distinct from the other tested species of Cephalosporium, Phialophora sensu lato and members of Gaeumannomyces-Harpophora species complex, which supports its classification as Harpophora maydis. Oligonucleotide primers for H. maydis were developed that can be used in a PCR diagnostic protocol to rapidly and reliably detect and identify this pathogen. These diagnostic PCR primers will aid the detection of H. maydis in diseased maize because this fungus can be difficult to detect and isolate, and the movement of authentic cultures may be limited by quarantine restrictions.

Proteomic Analysis of the Relationship between Metabolism and Nonhost Resistance in Soybean Exposed to Bipolaris maydis.

PubMed

Dong, Yumei; Su, Yuan; Yu, Ping; Yang, Min; Zhu, Shusheng; Mei, Xinyue; He, Xiahong; Pan, Manhua; Zhu, Youyong; Li, Chengyun

2015-01-01

Nonhost resistance (NHR) pertains to the most common form of plant resistance against pathogenic microorganisms of other species. Bipolaris maydis is a non-adapted pathogen affecting soybeans, particularly of maize/soybean intercropping systems. However, no experimental evidence has described the immune response of soybeans against B. maydis. To elucidate the molecular mechanism underlying NHR in soybeans, proteomics analysis based on two-dimensional polyacrylamide gel electrophoresis (2-DE) was performed to identify proteins involved in the soybean response to B. maydis. The spread of B. maydis spores across soybean leaves induced NHR throughout the plant, which mobilized almost all organelles and various metabolic processes in response to B. maydis. Some enzymes, including ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), mitochondrial processing peptidase (MPP), oxygen evolving enhancer (OEE), and nucleoside diphosphate kinase (NDKs), were found to be related to NHR in soybeans. These enzymes have been identified in previous studies, and STRING analysis showed that most of the protein functions related to major metabolic processes were induced as a response to B. maydis, which suggested an array of complex interactions between soybeans and B. maydis. These findings suggest a systematic NHR against non-adapted pathogens in soybeans. This response was characterized by an overlap between metabolic processes and response to stimulus. Several metabolic processes provide the soybean with innate immunity to the non-adapted pathogen, B. maydis. This research investigation on NHR in soybeans may foster a better understanding of plant innate immunity, as well as the interactions between plant and non-adapted pathogens in intercropping systems.

Proteomic Analysis of the Relationship between Metabolism and Nonhost Resistance in Soybean Exposed to Bipolaris maydis

PubMed Central

Dong, Yumei; Su, Yuan; Yu, Ping; Yang, Min; Zhu, Shusheng; Mei, Xinyue; He, Xiahong; Pan, Manhua; Zhu, Youyong; Li, Chengyun

2015-01-01

Nonhost resistance (NHR) pertains to the most common form of plant resistance against pathogenic microorganisms of other species. Bipolaris maydis is a non-adapted pathogen affecting soybeans, particularly of maize/soybean intercropping systems. However, no experimental evidence has described the immune response of soybeans against B. maydis. To elucidate the molecular mechanism underlying NHR in soybeans, proteomics analysis based on two-dimensional polyacrylamide gel electrophoresis (2-DE) was performed to identify proteins involved in the soybean response to B. maydis. The spread of B. maydis spores across soybean leaves induced NHR throughout the plant, which mobilized almost all organelles and various metabolic processes in response to B. maydis. Some enzymes, including ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), mitochondrial processing peptidase (MPP), oxygen evolving enhancer (OEE), and nucleoside diphosphate kinase (NDKs), were found to be related to NHR in soybeans. These enzymes have been identified in previous studies, and STRING analysis showed that most of the protein functions related to major metabolic processes were induced as a response to B. maydis, which suggested an array of complex interactions between soybeans and B. maydis. These findings suggest a systematic NHR against non-adapted pathogens in soybeans. This response was characterized by an overlap between metabolic processes and response to stimulus. Several metabolic processes provide the soybean with innate immunity to the non-adapted pathogen, B. maydis. This research investigation on NHR in soybeans may foster a better understanding of plant innate immunity, as well as the interactions between plant and non-adapted pathogens in intercropping systems. PMID:26513657

Ustilago echinata: Infection in a Mixed Martial Artist Following an Open Fracture.

PubMed

Stewart, Ethan; Waldman, Sarah; Sutton, Deanna A; Sanders, Carmita; Lindner, Jonathan; Fan, Hongxin; Wiederhold, Nathan P; Thompson, George R

2016-04-01

Ustilago, a common fungal parasite of grains, is infrequently isolated as a pathogen in humans. We describe a case of Ustilago echinata infection following an open distal tibia fracture, review the current literature of this genus as a cause of invasive fungal infection in humans, and discuss management issues.

Inhibition of non-enzymatic glycation by silk extracts from a Mexican land race and modern inbred lines of maize (Zea mays).

PubMed

Farsi, Darius Arthur; Harris, Cory S; Reid, Lana; Bennett, Steffany A L; Haddad, Pierre S; Martineau, Louis C; Arnason, John Thor

2008-01-01

Non-enzymatic glycation and the accumulation of advanced glycation end products (AGEs) are associated with various disease states, including complications of diabetes and aging. Secondary metabolites from several plant species are known to inhibit non-enzymatic glycation and the formation of AGEs, including flavonoids found in the style (silk) of Zea mays (maize). Thirteen modern maize inbreds and one land race were tested for in vitro inhibition of non-enzymatic glycation of bovine serum albumin. Many of the tested extracts exhibited inhibitory activity, in particular the newest inbreds, which were bred for resistance to gibberella ear rot (Fusarium graminearum) and common smut (Ustilago maydis). The most active maize genotype (CO441), displaying an IC50 of 9.5 microg/mL, was more effective than aminoguanidine, a known inhibitor of glycation. Zapalote chico, a land race with high maysin content, showed only moderate inhibitory activity compared with the modern maize genotypes. Antiglycation activity was highly correlated with the total phenolic content of silk extracts and mildly correlated with resistance to certain fungal infections. The results identify modern resistant and high phenolic maize inbreds as promising candidates for the development of natural AGE inhibitors for the prevention and treatment of diabetic complications and the degenerative effects of aging. Copyright (c) 2007 John Wiley & Sons, Ltd.

Expressed sequence tags from the flower pathogen Claviceps purpurea.

PubMed

Oeser, Birgitt; Beaussart, François; Haarmann, Thomas; Lorenz, Nicole; Nathues, Eva; Rolke, Yvonne; Scheffer, Jan; Weiner, January; Tudzynski, Paul

2009-09-01

SUMMARY The ascomycete Claviceps purpurea (ergot) is a biotrophic flower pathogen of rye and other grasses. The deleterious toxic effects of infected rye seeds on humans and grazing animals have been known since the Middle Ages. To gain further insight into the molecular basis of this disease, we generated about 10 000 expressed sequence tags (ESTs)-about 25% originating from axenic fungal culture and about 75% from tissues collected 6-20 days after infection of rye spikes. The pattern of axenic vs. in planta gene expression was compared. About 200 putative plant genes were identified within the in planta library. A high percentage of these were predicted to function in plant defence against the ergot fungus and other pathogens, for example pathogenesis-related proteins. Potential fungal pathogenicity and virulence genes were found via comparison with the pathogen-host interaction database (PHI-base; http://www.phi-base.org) and with genes known to be highly expressed in the haustoria of the bean rust fungus. Comparative analysis of Claviceps and two other fungal flower pathogens (necrotrophic Fusarium graminearum and biotrophic Ustilago maydis) highlighted similarities and differences in their lifestyles, for example all three fungi have signalling components and cell wall-degrading enzymes in their arsenal. In summary, the analysis of axenic and in planta ESTs yielded a collection of candidate genes to be evaluated for functional roles in this plant-microbe interaction.

Interpreting diplodiosis: bioactive metabolites in Stenocarpella maydis ear rot of maize

USDA-ARS?s Scientific Manuscript database

Stenocarpella maydis is a fungal pathogen of major importance that causes a dry-rot of maize ears and is associated with a neuromycotoxicosis in cattle grazing harvested maize fields in southern Africa and Argentina. Chemical investigations of S. maydis rotted kernels at harvest in Illinois led to t...

Diplodiatoxin, chaetoglobosins, and diplonine associated with a field outbreak of Stenocarpella ear rot in Illinois.

PubMed

Rogers, Kristina D; Cannistra, Joseph C; Gloer, James B; Wicklow, Donald T

2014-05-01

Stenocarpella maydis causes a fungal dry-rot of maize ears and is associated with diplodiosis, a neuromycotoxicosis in cattle grazing harvested maize fields in southern Africa and Argentina. There have been no reports of Stenocarpella metabolites in maize crop residues. Chemical investigations of S. maydis-infected grain from ears exhibiting different levels of ear rot severity following a 2010 field outbreak of Stenocarpella ear rot in Illinois led to the detection of diplodiatoxin and chaetoglobosins M and O as major components in the ethyl acetate extracts by LC-MS. Following post-harvest moist incubation of the S. maydis-infected grain, the amounts of each compound increased (approx. tenfold) and chaetoglobosin K was detected as a dominant toxin. In separate (1)H NMR-based analyses, the neurotoxin diplonine was detected as a minor component in methanol extracts of S. maydis-infected grain as well as cultures of S. maydis isolates from Midwest corn. Proline betaine (=stachydrine) and glycine betaine were also detected in these extracts as major components. This constitutes the first report of chaetoglobosin M, chaetoglobosin O, proline betaine, or glycine betaine from S. maydis, and the first record of diplodiatoxin, diplonine, proline betaine, glycine betaine, or chaetoglobosins M, O, or K being associated with a natural field outreak of S. maydis ear rot.

Bioactive metabolites from Stenocarpella maydis, a stalk and ear rot pathogen of maize

USDA-ARS?s Scientific Manuscript database

Stenocarpella maydis is a fungal pathogen of major importance that causes a dry-rot of maize ears and is associated with a neuromycotoxicosis in cattle grazing harvested maize fields in southern Africa and Argentina. In an effort to investigate the potential roles of S. maydis metabolites in the fun...

Influence of Stenocarpella maydis infected corn on the composition of corn kernel and its conversion into ethanol

USDA-ARS?s Scientific Manuscript database

Widespread epidemics of Stenocarpella ear rot (formerly Diplodia ear rot) have occurred throughout the central U.S. Corn Belt in recent years, but the influence of S. maydis infected grain on corn ethanol production is unknown. In this study, S. maydis infected ears of variety 'Heritage 4646' were h...

Allozyme-Specific Modification of a Maize Seed Chitinase by a Protein Secreted by the Fungal Pathogen Stenocarpella maydis

USDA-ARS?s Scientific Manuscript database

Stenocarpella maydis causes both dry-ear rot and stalk rot of maize. Maize inbreds have varying levels of resistance to S. maydis ear rot. The genetic basis of resistance appears to rely on multiple genetic factors, none of which are known. The commonly used stiff stalk inbred B73 has been shown ...

Pathogen Trojan Horse Delivers Bioactive Host Protein to Alter Maize Anther Cell Behavior in Situ.

PubMed

van der Linde, Karina; Timofejeva, Ljudmilla; Egger, Rachel L; Ilau, Birger; Hammond, Reza; Teng, Chong; Meyers, Blake C; Doehlemann, Gunther; Walbot, Virginia

2018-03-01

Small proteins are crucial signals during development, host defense, and physiology. The highly spatiotemporal restricted functions of signaling proteins remain challenging to study in planta. The several month span required to assess transgene expression, particularly in flowers, combined with the uncertainties from transgene position effects and ubiquitous or overexpression, makes monitoring of spatiotemporally restricted signaling proteins lengthy and difficult. This situation could be rectified with a transient assay in which protein deployment is tightly controlled spatially and temporally in planta to assess protein functions, timing, and cellular targets as well as to facilitate rapid mutagenesis to define functional protein domains. In maize ( Zea mays ), secreted ZmMAC1 (MULTIPLE ARCHESPORIAL CELLS1) was proposed to trigger somatic niche formation during anther development by participating in a ligand-receptor module. Inspired by Homer's Trojan horse myth, we engineered a protein delivery system that exploits the secretory capabilities of the maize smut fungus Ustilago maydis , to allow protein delivery to individual cells in certain cell layers at precise time points. Pathogen-supplied ZmMAC1 cell-autonomously corrected both somatic cell division and differentiation defects in mutant Zm mac1-1 anthers. These results suggest that exploiting host-pathogen interactions may become a generally useful method for targeting host proteins to cell and tissue types to clarify cellular autonomy and to analyze steps in cell responses. © 2018 American Society of Plant Biologists. All rights reserved.

Binding of the host-specific toxins from Helminthosporium maydis race T and Phyllosticta maydis to mitochondria isolated from Zea mays

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

Frantzen, K.A.

1985-01-01

Helminthosphorium maydis race I and Phyllosticta maydis, the causal agents of southern and yellow corn leaf blights, respectively, produce host-specific toxins. The toxic specificity of these natural products is identical to the host-specificity of the pathogens for certain varieties of corn. Susceptible genotypes carry the Texas type of cytoplasmic male sterility. Isolated mitochondria from susceptible plant species are highly sensitive to these toxins, whereas other plant species, including resistant corn varieties, and their mitochondria are not. The mitochondrion may be the primary cellular site of action for these toxins. The toxins from H. maydis and P. maydis were tritiated bymore » reduction with borotritide salts. The labeled products had a high specific activity (3.8 to 8 Ci/mmole), high biological activity, and specificity identical to that of the native toxins. A filtration binding assay was developed to investigate the binding characteristics of these labeled toxins to isolated mitochondria. Mitochondria isolated from both cytoplasmic male sterile (Texas) and normal corn demonstrated similar binding characteristics including ligand displaceable binding with both labeled toxins. Ligand displaceable binding was also detectable in mitochondria from soybeans, a nonhost plant for these fungi. The ability to displace the bound labeled toxins was generally correlated with the biological activity of the competing toxin. The results of this study suggest that a receptor site hypothesis for the mode of action of these toxins may not be valid.« less

Amplified Fragment Length Polymorphism Diversity in Cephalosporium maydis from Egypt.

PubMed

Saleh, Amgad A; Zeller, Kurt A; Ismael, Abou-Serie M; Fahmy, Zeinab M; El-Assiuty, Elhamy M; Leslie, John F

2003-07-01

ABSTRACT Cephalosporium maydis, the causal agent of late wilt of maize, was first described in Egypt in the 1960s, where it can cause yield losses of up to 40% in susceptible plantings. We characterized 866 isolates of C. maydis collected from 14 governates in Egypt, 7 in the Nile River Delta and 7 in southern (Middle and Upper) Egypt, with amplified fragment length polymorphism (AFLP) markers. The four AFLP primer-pair combinations generated 68 bands, 25 of which were polymorphic, resulting in 52 clonal haplotypes that clustered the 866 isolates into four phylogenetic lineages. Three lineages were found in both the Nile River Delta and southern Egypt. Lineage IV, the most diverse group (20 haplotypes), was recovered only from governates in the Nile River Delta. In some locations, one lineage dominated (up to 98% of the isolates recovered) and, from some fields, only a single haplotype was recovered. Under field conditions in Egypt, there is no evidence that C. maydis reproduces sexually. The nonuniform geographic distribution of the pathogen lineages within the country could be due to differences in climate or in the farming system, because host material differs in susceptibility and C. maydis lineages differ in pathogenicity.

The role of certain oxidative enzymes, catalase, and beta-glucosidase on virulence of Cephalosporium maydis.

PubMed

Abd-Elrazik, A; Darweish, F A; Rushdi, M H

1978-01-01

Isolates of Cephalosporium maydis varied in their pathogenicity to D.C. 67 maize cultivar from highly to weakly pathogenic. Highly pathogenic isolates showed lower activity of polyphenol oxidase, peroxidase, cytochrome oxidase, and beta-glucosidase enzymes and higher activity of catalase and dehydrogenase than weakly pathogenic isolates. Enzymes production by the tested isolates increased as the culture age increased; except in case of catalase enzyme, the reverse action was detected. The role of these enzymes in the virulence of C. maydis is suggested and discussed.

Siderophores as iron storage compounds in the yeasts Rhodotorula minuta and Ustilago sphaerogena detected by in vivo Mössbauer spectroscopy

NASA Astrophysics Data System (ADS)

Matzanke, B. F.; Bill, E.; Trautwein, A. X.; Winkelmann, G.

1990-07-01

In the yeasts Rhodotorula minuta and Ustilago sphaerogena siderophores represent the main intracellular iron pool. We suggest a ferritin substituting function of these siderophores in addition to their role as iron transport agents. In Rhodotorula transport and storage siderophore is the same compound whereas in Ustilago the iron-storage siderophore is ferrichrome. Besides siderophores, merely two iron metabolites can be observed. Other iron-requiring compounds are at least one order of magnitude less abundant in these yeasts. The ferrous metabolite has been detected in many other microbial systems and seems to be of general occurence and importance.

Identification of multiple ear-colonizing insect and disease resistance in CIMMYT maize inbred lines with varying levels of silk maysin.

PubMed

Ni, Xinzhi; Krakowsky, Matthew D; Buntin, G David; Rector, Brian G; Guo, Baozhu; Snook, Maurice E

2008-08-01

Ninety four corn inbred lines selected from International Center for the Improvement of Maize and Wheat (CIMMYT) in Mexico were evaluated for levels of silk maysin in 2001 and 2002. Damage by major ear-feeding insects [i.e., corn earworm, Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae); maize weevil, Sitophilus zeamais (Motschulsky) (Coleoptera: Curculionidae); brown stink bug, Euschistus servus (Say); southern green stink bugs, Nezara viridula (L.) (Heteroptera: Pentatomidae)], and common smut [Ustilago maydis DC (Corda)] infection on these inbred lines were evaluated in 2005 and 2006 under subtropical conditions at Tifton, GA. Ten inbred lines possessing good agronomic traits were also resistant to the corn earworm. The correlation between ear-feeding insect damage or smut infection and three phenotypic traits (silk maysin level, husk extension, and husk tightness of corn ears) was also examined. Corn earworm and stink bug damage was negatively correlated to husk extension, but not to either silk maysin levels or husk tightness. In combination with the best agronomic trait ratings that show the least corn earworm and stink bug damage, lowest smut infection rate, and good insect-resistant phenotypic traits (i.e., high maysin and good husk coverage and husk tightness), 10 best inbred lines (CML90, CML92, CML94, CML99, CML104, CML108, CML114, CML128, CML137, and CML373) were identified from the 94 lines examined. These selected inbred lines will be used for further examination of their resistance mechanisms and development of new corn germplasm that confers multiple ear-colonizing pest resistance.

Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens.

PubMed

Xu, Jun; Saunders, Charles W; Hu, Ping; Grant, Raymond A; Boekhout, Teun; Kuramae, Eiko E; Kronstad, James W; Deangelis, Yvonne M; Reeder, Nancy L; Johnstone, Kevin R; Leland, Meredith; Fieno, Angela M; Begley, William M; Sun, Yiping; Lacey, Martin P; Chaudhary, Tanuja; Keough, Thomas; Chu, Lien; Sears, Russell; Yuan, Bo; Dawson, Thomas L

2007-11-20

Fungi in the genus Malassezia are ubiquitous skin residents of humans and other warm-blooded animals. Malassezia are involved in disorders including dandruff and seborrheic dermatitis, which together affect >50% of humans. Despite the importance of Malassezia in common skin diseases, remarkably little is known at the molecular level. We describe the genome, secretory proteome, and expression of selected genes of Malassezia globosa. Further, we report a comparative survey of the genome and secretory proteome of Malassezia restricta, a close relative implicated in similar skin disorders. Adaptation to the skin environment and associated pathogenicity may be due to unique metabolic limitations and capabilities. For example, the lipid dependence of M. globosa can be explained by the apparent absence of a fatty acid synthase gene. The inability to synthesize fatty acids may be complemented by the presence of multiple secreted lipases to aid in harvesting host lipids. In addition, an abundance of genes encoding secreted hydrolases (e.g., lipases, phospholipases, aspartyl proteases, and acid sphingomyelinases) was found in the M. globosa genome. In contrast, the phylogenetically closely related plant pathogen Ustilago maydis encodes a different arsenal of extracellular hydrolases with more copies of glycosyl hydrolase genes. M. globosa shares a similar arsenal of extracellular hydrolases with the phylogenetically distant human pathogen, Candida albicans, which occupies a similar niche, indicating the importance of host-specific adaptation. The M. globosa genome sequence also revealed the presence of mating-type genes, providing an indication that Malassezia may be capable of sex.

Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens

PubMed Central

Xu, Jun; Saunders, Charles W.; Hu, Ping; Grant, Raymond A.; Boekhout, Teun; Kuramae, Eiko E.; Kronstad, James W.; DeAngelis, Yvonne M.; Reeder, Nancy L.; Johnstone, Kevin R.; Leland, Meredith; Fieno, Angela M.; Begley, William M.; Sun, Yiping; Lacey, Martin P.; Chaudhary, Tanuja; Keough, Thomas; Chu, Lien; Sears, Russell; Yuan, Bo; Dawson, Thomas L.

2007-01-01

Fungi in the genus Malassezia are ubiquitous skin residents of humans and other warm-blooded animals. Malassezia are involved in disorders including dandruff and seborrheic dermatitis, which together affect >50% of humans. Despite the importance of Malassezia in common skin diseases, remarkably little is known at the molecular level. We describe the genome, secretory proteome, and expression of selected genes of Malassezia globosa. Further, we report a comparative survey of the genome and secretory proteome of Malassezia restricta, a close relative implicated in similar skin disorders. Adaptation to the skin environment and associated pathogenicity may be due to unique metabolic limitations and capabilities. For example, the lipid dependence of M. globosa can be explained by the apparent absence of a fatty acid synthase gene. The inability to synthesize fatty acids may be complemented by the presence of multiple secreted lipases to aid in harvesting host lipids. In addition, an abundance of genes encoding secreted hydrolases (e.g., lipases, phospholipases, aspartyl proteases, and acid sphingomyelinases) was found in the M. globosa genome. In contrast, the phylogenetically closely related plant pathogen Ustilago maydis encodes a different arsenal of extracellular hydrolases with more copies of glycosyl hydrolase genes. M. globosa shares a similar arsenal of extracellular hydrolases with the phylogenetically distant human pathogen, Candida albicans, which occupies a similar niche, indicating the importance of host-specific adaptation. The M. globosa genome sequence also revealed the presence of mating-type genes, providing an indication that Malassezia may be capable of sex. PMID:18000048

A comparison of on-line and off-line bioaerosol measurements at a biowaste site.

PubMed

Feeney, Patrick; Rodríguez, Santiago Fernández; Molina, Rafael; McGillicuddy, Eoin; Hellebust, Stig; Quirke, Michael; Daly, Shane; O'Connor, David; Sodeau, John

2018-06-01

An air measurement campaign was carried out at a green-waste composting site in the South of Ireland during Spring 2016. The aim was to quantify and identify the levels of Primary Biological Aerosol Particles (PBAP) that were present using the traditional off-line, impaction/optical microscopy method alongside an on-line, spectroscopic approach termed WIBS (Wideband Integrated Bioaerosol Sensor), which can provide number concentrations, sizes and "shapes" of airborne PBAP in real-time by use of Light Induced Fluorescence (LIF). The results from the two techniques were compared in order to validate the use of the spectroscopic method for determining the releases of the wide-range of PBAP present there as a function of site activity and meteorological conditions. The seven-day monitoring period undertaken was much longer than any real-time studies that have been previously performed and allowed due comparison between weekday (working) activities at the site and weekend (closed) releases. The time-span also allowed relationships between site activities like turning, agitation or waste delivery and the WIBS data to be determined in a quantitative manner. This information cannot be obtained with the Andersen Sampling methods generally employed at green-waste management sites. Furthermore, few specific bioaerosol types other than Aspergillus fumigatus, are identified using the traditional protocols employed for site licensing purposes. Here though the co-location of WIBS with the impaction instrument made it possible to identify the real-time release behaviour of a specific plant pathogenic spore, Ustilago maydis, present after green-waste deliveries were made by a local distillery. Copyright © 2018 Elsevier Ltd. All rights reserved.

Online monitoring of fermentation processes via non-invasive low-field NMR.

PubMed

Kreyenschulte, Dirk; Paciok, Eva; Regestein, Lars; Blümich, Bernhard; Büchs, Jochen

2015-09-01

For the development of biotechnological processes in academia as well as in industry new techniques are required which enable online monitoring for process characterization and control. Nuclear magnetic resonance (NMR) spectroscopy is a promising analytical tool, which has already found broad applications in offline process analysis. The use of online monitoring, however, is oftentimes constrained by high complexity of custom-made NMR bioreactors and considerable costs for high-field NMR instruments (>US$200,000). Therefore, low-field (1) H NMR was investigated in this study in a bypass system for real-time observation of fermentation processes. The new technique was validated with two microbial systems. For the yeast Hansenula polymorpha glycerol consumption could accurately be assessed in spite of the presence of high amounts of complex constituents in the medium. During cultivation of the fungal strain Ustilago maydis, which is accompanied by the formation of several by-products, the concentrations of glucose, itaconic acid, and the relative amount of glycolipids could be quantified. While low-field spectra are characterized by reduced spectral resolution compared to high-field NMR, the compact design combined with the high temporal resolution (15 s-8 min) of spectra acquisition allowed online monitoring of the respective processes. Both applications clearly demonstrate that the investigated technique is well suited for reaction monitoring in opaque media while at the same time it is highly robust and chemically specific. It can thus be concluded that low-field NMR spectroscopy has a great potential for non-invasive online monitoring of biotechnological processes at the research and practical industrial scales. © 2015 Wiley Periodicals, Inc.

Sequence and phylogenetic analyses of novel totivirus-like double-stranded RNAs from field-collected powdery mildew fungi.

PubMed

Kondo, Hideki; Hisano, Sakae; Chiba, Sotaro; Maruyama, Kazuyuki; Andika, Ida Bagus; Toyoda, Kazuhiro; Fujimori, Fumihiro; Suzuki, Nobuhiro

2016-02-02

The identification of mycoviruses contributes greatly to understanding of the diversity and evolutionary aspects of viruses. Powdery mildew fungi are important and widely studied obligate phytopathogenic agents, but there has been no report on mycoviruses infecting these fungi. In this study, we used a deep sequencing approach to analyze the double-stranded RNA (dsRNA) segments isolated from field-collected samples of powdery mildew fungus-infected red clover plants in Japan. Database searches identified the presence of at least ten totivirus (genus Totivirus)-like sequences, termed red clover powdery mildew-associated totiviruses (RPaTVs). The majority of these sequences shared moderate amino acid sequence identity with each other (<44%) and with other known totiviruses (<59%). Nine of these identified sequences (RPaTV1a, 1b and 2-8) resembled the genome of the prototype totivirus, Saccharomyces cerevisiae virus-L-A (ScV-L-A) in that they contained two overlapping open reading frames (ORFs) encoding a putative coat protein (CP) and an RNA dependent RNA polymerase (RdRp), while one sequence (RPaTV9) showed similarity to another totivirus, Ustilago maydis virus H1 (UmV-H1) that encodes a single polyprotein (CP-RdRp fusion). Similar to yeast totiviruses, each ScV-L-A-like RPaTV contains a -1 ribosomal frameshift site downstream of a predicted pseudoknot structure in the overlapping region of these ORFs, suggesting that the RdRp is translated as a CP-RdRp fusion. Moreover, several ScV-L-A-like sequences were also found by searches of the transcriptome shotgun assembly (TSA) libraries from rust fungi, plants and insects. Phylogenetic analyses show that nine ScV-L-A-like RPaTVs along with ScV-L-A-like sequences derived from TSA libraries are clustered with most established members of the genus Totivirus, while one RPaTV forms a new distinct clade with UmV-H1, possibly establishing an additional genus in the family. Taken together, our results indicate the presence of diverse, novel totiviruses in the powdery mildew fungus populations infecting red clover plants in the field. Copyright © 2015 Elsevier B.V. All rights reserved.

Knowledge and use of edible mushrooms in two municipalities of the Sierra Tarahumara, Chihuahua, Mexico.

PubMed

Quiñónez-Martínez, Miroslava; Ruan-Soto, Felipe; Aguilar-Moreno, Ivonne Estela; Garza-Ocañas, Fortunato; Lebgue-Keleng, Toutcha; Lavín-Murcio, Pablo Antonio; Enríquez-Anchondo, Irma Delia

2014-09-17

The Sierra Madre Occidental of Chihuahua in Northern Mexico is inhabited by indigenous Raramuris, mestizos, and other ethnic groups. The territory consists of canyons and ravines with pine, oak and pine-oak forests in the higher plateaus. A great diversity of potentially edible mushrooms is found in forests of the Municipalities of Bocoyna and Urique. Their residents are the only consumers of wild mushrooms in the Northern Mexico; they have a long tradition of collecting and eating these during the "rainy season." However, despite the wide diversity of edible mushrooms that grow in these areas, residents have a selective preference. This paper aims to record evidence of the knowledge and use of wild potentially edible mushroom species by inhabitants of towns in the Sierra Tarahumara of Chihuahua, Mexico. Using a semi-structured technique, we surveyed 197 habitants from seven locations in Urique, Bocoyna, and the Cusarare area from 2010 to 2012. Known fungi, local nomenclature, species consumed, preparation methods, appreciation of taste, forms of preservation, criteria for differentiating toxic and edible fungi, other uses, economic aspects, and traditional teaching were recorded. To identify the recognized species, photographic stimuli of 22 local edible species and two toxic species were used. The respondents reported preference for five species: Amanita rubescens, Agaricus campestris, Ustilago maydis, Hypomyces lactifluorum, and the Amanita caesarea complex. No apparent differences were found between ethnic groups in terms of preference, although mestizos used other species in Bocoyna (Boletus edulis and B. pinophilus). Some different uses of fungi are recognized by respondents, i.e. home decorations, medicine, as food in breeding rams, etc. The studied population shows a great appreciation towards five species, mainly the A. caesarea complex, and an apparent lack of knowledge of nearly 20 species which are used as food in other areas of Mexico. There are no apparent differences among Sierra inhabitants in terms of gender, occupation, or language regarding the recognition and consumption of species. The rejection of certain species is due mainly to fear of poisoning and the traditional selective teaching of families in the mountain communities of the Sierra Tarahumara.

Evidence for resistance polymorphism in the Bromus tectorum/Ustilago bullata pathosystem: implications for biocontrol

Treesearch

S. E. Meyer; D. L. Nelson; S. Clement

2001-01-01

Bromus tectorum L. (cheatgrass or downy brome) is an important exotic weed in natural ecosystems as well as in winter cereal cropland in semiarid western North America. The systemic, seedling-infecting head smut pathogen Ustilago bullata Berk. commonly infects cheatgrass stands, often at epidemic levels. We examined factors...

The corn blight problem: 1970 and 1971

NASA Technical Reports Server (NTRS)

Bauer, M. E.

1972-01-01

Southern corn leaf blight is caused by the fungus, Helminthosporium maydis. Race T of H maydis adapted itself to the Texas male sterile cytoplasm corn. The problems caused by this variety of the blight in 1970 and 1971 are discussed, as well as the symptoms and development of the disease.

Ecological genetics of the Bromus tectorum (Poaceae) - Ustilago Bullata (Ustilaginaceae): A role for frequency dependent selection?

Treesearch

Susan E. Meyer; David L. Nelson; Suzette Clement; Alisa Ramakrishnan

2010-01-01

Evolutionary processes that maintain genetic diversity in plants are likely to include selection imposed by pathogens. Negative frequency-dependent selection is a mechanism for maintenance of resistance polymorphism in plant - pathogen interactions. We explored whether such selection operates in the Bromus tectorum - Ustilago bullata pathosystem. Gene-for-gene...

Impact of applying edible oils to silk channels on ear pests of sweet corn.

PubMed

Ni, Xinzhi; Sparks, Alton N; Riley, David G; Li, Xianchun

2011-06-01

The impact of applying edible oils to corn silks on ear-feeding insects in sweet corn, Zea mays L., production was evaluated in 2006 and 2007. Six edible oils used in this experiment were canola, corn, olive, peanut, sesame, and soybean. Water and two commercial insecticidal oils (Neemix neem oil and nC21 Sunspray Ultrafine, a horticultural mineral oil) were used as the controls for the experiment. Six parameters evaluated in this experiment were corn earworm [Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae)] damage rating, the number of sap beetle [Carpophilus spp. (Coleoptera: Nitidulidae)] adults and larvae, the number of corn silk fly (or picture-winged fly) (Diptera: Ulidiidae) larvae, common smut [Ustilago maydis (D.C.) Corda] infection rate, and corn husk coverage. Among the two control treatments, neem oil reduced corn earworm damage at both pre- and postpollination applications in 2006, but not in 2007, whereas the mineral oil applied at postpollination treatments reduced corn earworm damage in both years. The mineral oil also reduced the number of sap beetle adults, whereas the neem oil applied at postpollination attracted the most sap beetle adults in 2007. Among the six edible oil treatments, the corn and sesame oils applied at postpollination reduced corn earworm damage only in 2007. The application of the peanut oil at postpollination attracted more sap beetle adults in 2006, and more sap beetle larvae in 2007. Olive and neem oils significantly reduced husk coverage compared with the water control in both years. The mineral oil application consistently increased smut infection rate in both 2006 and 2007. Ramifications of using oil treatments in ear pest management also are discussed.

The 3-hydroxy-3-methylglutaryl coenzyme-A reductases from fungi: a proposal as a therapeutic target and as a study model.

PubMed

Andrade-Pavón, Dulce; Sánchez-Sandoval, Eugenia; Rosales-Acosta, Blanca; Ibarra, José Antonio; Tamariz, Joaquín; Hernández-Rodríguez, César; Villa-Tanaca, Lourdes

2014-01-01

The enzyme 3-hydroxy-3-methylglutaryl coenzyme-A reductase (HMGR) catalyzes the conversion of HMG-Co-A into mevalonate. This step is the limiting point for the synthesis of cholesterol in mammals and ergosterol in fungi. We describe in this article the genome organization of HMGR coding genes and those deduced from different fungi, recount the evidence showing statins as HMGR inhibitors for ergosterol synthesis and its effect in yeast viability, and propose fungal HMGR (HMGRf) as a model to study the use of pharmaceutical compounds to inhibit cholesterol and ergosterol synthesis. Bibliographical search and bioinformatic analyses were performed and discussed. HMGRfs belong to the class I with a high homology in the catalytic region. The sterol biosynthetic pathway in humans and fungi share many enzymes in the initial steps (such as the HMGR enzyme), but in the last steps enzymes are different rendering the two final products: cholesterol in mammals and ergosterol in fungi. With regards to inhibitors such as statins and other compounds, these affect also fungal viability. Since HMGR from Schizosaccharomyces pombe and Ustilago maydis are very similar to the human HMGR in the catalytic regions, we propose that fungal enzymes can be used to test inhibitors for a potential use in humans. We consider that HMGRf is a good therapeutic target to design and test new antifungal compounds. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

Common Motifs in the Response of Cereal Primary Metabolism to Fungal Pathogens are not Based on Similar Transcriptional Reprogramming

PubMed Central

Voll, Lars Matthias; Horst, Robin Jonathan; Voitsik, Anna-Maria; Zajic, Doreen; Samans, Birgit; Pons-Kühnemann, Jörn; Doehlemann, Gunther; Münch, Steffen; Wahl, Ramon; Molitor, Alexandra; Hofmann, Jörg; Schmiedl, Alfred; Waller, Frank; Deising, Holger Bruno; Kahmann, Regine; Kämper, Jörg; Kogel, Karl-Heinz; Sonnewald, Uwe

2011-01-01

During compatible interactions with their host plants, biotrophic plant–pathogens subvert host metabolism to ensure the sustained provision of nutrient assimilates by the colonized host cells. To investigate, whether common motifs can be revealed in the response of primary carbon and nitrogen metabolism toward colonization with biotrophic fungi in cereal leaves, we have conducted a combined metabolome and transcriptome study of three quite divergent pathosystems, the barley powdery mildew fungus (Blumeria graminis f.sp. hordei), the corn smut fungus Ustilago maydis, and the maize anthracnose fungus Colletotrichum graminicola, the latter being a hemibiotroph that only exhibits an initial biotrophic phase during its establishment. Based on the analysis of 42 water-soluble metabolites, we were able to separate early biotrophic from late biotrophic interactions by hierarchical cluster analysis and principal component analysis, irrespective of the plant host. Interestingly, the corresponding transcriptome dataset could not discriminate between these stages of biotrophy, irrespective, of whether transcript data for genes of central metabolism or the entire transcriptome dataset was used. Strong differences in the transcriptional regulation of photosynthesis, glycolysis, the TCA cycle, lipid biosynthesis, and cell wall metabolism were observed between the pathosystems. However, increased contents of Gln, Asn, and glucose as well as diminished contents of PEP and 3-PGA were common to early post-penetration stages of all interactions. On the transcriptional level, genes of the TCA cycle, nucleotide energy metabolism and amino acid biosynthesis exhibited consistent trends among the compared biotrophic interactions, identifying the requirement for metabolic energy and the rearrangement of amino acid pools as common transcriptional motifs during early biotrophy. Both metabolome and transcript data were employed to generate models of leaf primary metabolism during early biotrophy for the three investigated interactions. PMID:22645534

The cultural significance of wild mushrooms in San Mateo Huexoyucan, Tlaxcala, Mexico.

PubMed

Alonso-Aguilar, Luis Enrique; Montoya, Adriana; Kong, Alejandro; Estrada-Torres, Arturo; Garibay-Orijel, Roberto

2014-03-05

We performed an ethnomycological study in a community in Tlaxcala, Central Mexico to identify the most important species of wild mushrooms growing in an oak forest, their significance criteria, and to validate the Cultural Significance Index (CSI). Thirty-three mestizo individuals were randomly selected in San Mateo Huexoyucan and were asked seven questions based on criteria established by the CSI. Among the 49 mushroom species collected in the oak forest and open areas, 20 species were mentioned most often and were analyzed in more detail. Ordination and grouping techniques were used to determine the relationship between the cultural significance of the mushroom species, according to a perceived abundance index, frequency of use index, taste score appreciation index, multifunctional food index, knowledge transmission index, and health index. The mushrooms with highest CSI values were Agaricus campestris, Ramaria spp., Amanita aff. basii, Russula spp., Ustilago maydis, and Boletus variipes. These species were characterized by their good taste and were considered very nutritional. The species with the lowest cultural significance included Russula mexicana, Lycoperdon perlatum, and Strobylomyces strobilaceus. The ordination and grouping analyses identified four groups of mushrooms by their significance to the people of Huexoyucan. The most important variables that explained the grouping were the taste score appreciation index, health index, the knowledge transmission index, and the frequency of use index. A. aff. basii and A. campestris were the most significant wild mushrooms to the people of San Mateo. The diversity of the Russula species and the variety of Amanita and Ramaria species used by these people was outstanding. Environments outside the forest also produced useful resources. The CSI used in Oaxaca was useful for determining the cultural significance of mushrooms in SMH, Tlaxcala. This list of mushrooms can be used in conservation proposals for the Quercus forests in the area.

Identification of growth stage molecular markers in Trichoderma sp. 'atroviride type B' and their potential application in monitoring fungal growth and development in soil.

PubMed

Mendoza-Mendoza, Artemio; Steyaert, Johanna; Nieto-Jacobo, Maria Fernanda; Holyoake, Andrew; Braithwaite, Mark; Stewart, Alison

2015-11-01

Several members of the genus Trichoderma are biocontrol agents of soil-borne fungal plant pathogens. The effectiveness of biocontrol agents depends heavily on how they perform in the complex field environment. Therefore, the ability to monitor and track Trichoderma within the environment is essential to understanding biocontrol efficacy. The objectives of this work were to: (a) identify key genes involved in Trichoderma sp. 'atroviride type B' morphogenesis; (b) develop a robust RNA isolation method from soil; and (c) develop molecular marker assays for characterizing morphogenesis whilst in the soil environment. Four cDNA libraries corresponding to conidia, germination, vegetative growth and conidiogenesis were created, and the genes identified by sequencing. Stage specificity of the different genes was confirmed by either Northern blot or quantitative reverse-transcriptase PCR (qRT-PCR) analysis using RNA from the four stages. con10, a conidial-specific gene, was observed in conidia, as well as one gene also involved in subsequent stages of germination (L-lactate/malate dehydrogenase encoding gene). The germination stage revealed high expression rates of genes involved in amino acid and protein biosynthesis, while in the vegetative-growth stage, genes involved in differentiation, including the mitogen-activated protein kinase kinase similar to Kpp7 from Ustilago maydis and the orthologue to stuA from Aspergillus nidulans, were preferentially expressed. Genes involved in cell-wall synthesis were expressed during conidiogenesis. We standardized total RNA isolation from Trichoderma sp. 'atroviride type B' growing in soil and then examined the expression profiles of selected genes using qRT-PCR. The results suggested that the relative expression patterns were cyclic and not accumulative.

Gene Network Polymorphism Illuminates Loss and Retention of Novel RNAi Silencing Components in the Cryptococcus Pathogenic Species Complex.

PubMed

Feretzaki, Marianna; Billmyre, R Blake; Clancey, Shelly Applen; Wang, Xuying; Heitman, Joseph

2016-03-01

RNAi is a ubiquitous pathway that serves central functions throughout eukaryotes, including maintenance of genome stability and repression of transposon expression and movement. However, a number of organisms have lost their RNAi pathways, including the model yeast Saccharomyces cerevisiae, the maize pathogen Ustilago maydis, the human pathogen Cryptococcus deuterogattii, and some human parasite pathogens, suggesting there may be adaptive benefits associated with both retention and loss of RNAi. By comparing the RNAi-deficient genome of the Pacific Northwest Outbreak C. deuterogattii strain R265 with the RNAi-proficient genomes of the Cryptococcus pathogenic species complex, we identified a set of conserved genes that were lost in R265 and all other C. deuterogattii isolates examined. Genetic and molecular analyses reveal several of these lost genes play roles in RNAi pathways. Four novel components were examined further. Znf3 (a zinc finger protein) and Qip1 (a homolog of N. crassa Qip) were found to be essential for RNAi, while Cpr2 (a constitutive pheromone receptor) and Fzc28 (a transcription factor) are involved in sex-induced but not mitosis-induced silencing. Our results demonstrate that the mitotic and sex-induced RNAi pathways rely on the same core components, but sex-induced silencing may be a more specific, highly induced variant that involves additional specialized or regulatory components. Our studies further illustrate how gene network polymorphisms involving known components of key cellular pathways can inform identification of novel elements and suggest that RNAi loss may have been a core event in the speciation of C. deuterogattii and possibly contributed to its pathogenic trajectory.

Ultrastructure and phylogeny of Ustilago coicis *

PubMed Central

Zhang, Jing-ze; Guan, Pei-gang; Tao, Gang; Ojaghian, Mohammad Reza; Hyde, Kevin David

2013-01-01

Ustilago coicis causes serious smut on Coix lacryma-jobi in Dayang Town, Jinyun County, Zhejiang Province of China. In this paper, ultrastructural assessments on fungus-host interactions and teliospore development are presented, and molecular phylogenetic analyses have been done to elucidate the phylogenetic placement of the taxon. Hyphal growth within infected tissues was both intracellular and intercellular and on the surface of fungus-host interaction, and the fungal cell wall and the invaginated host plasma membrane were separated by a sheath comprising two distinct layers between the fungal cell wall and the invaginated host plasma membrane. Ornamentation development of teliospore walls was unique as they appeared to be originated from the exosporium. In addition, internal transcribed spacer (ITS) and large subunit (LSU) sequence data showed that U. coicis is closely related to Ustilago trichophora which infects grass species of the genus Echinochloa (Poaceae). PMID:23549851

Use of inter-simple sequence repeats and amplified fragment length polymorphisms to analyze genetic relationships among small grain-infecting species of ustilago.

PubMed

Menzies, J G; Bakkeren, G; Matheson, F; Procunier, J D; Woods, S

2003-02-01

ABSTRACT In the smut fungi, few features are available for use as taxonomic criteria (spore size, shape, morphology, germination type, and host range). DNA-based molecular techniques are useful in expanding the traits considered in determining relationships among these fungi. We examined the phylogenetic relationships among seven species of Ustilago (U. avenae, U. bullata, U. hordei, U. kolleri, U. nigra, U. nuda, and U. tritici) using inter-simple sequence repeats (ISSRs) and amplified fragment length polymorphisms (AFLPs) to compare their DNA profiles. Fifty-four isolates of different Ustilago spp. were analyzed using ISSR primers, and 16 isolates of Ustilago were studied using AFLP primers. The variability among isolates within species was low for all species except U. bullata. The isolates of U. bullata, U. nuda, and U. tritici were well separated and our data supports their speciation. U. avenae and U. kolleri isolates did not separate from each other and there was little variability between these species. U. hordei and U. nigra isolates also showed little variability between species, but the isolates from each species grouped together. Our data suggest that U. avenae and U. kolleri are monophyletic and should be considered one species, as should U. hordei and U. nigra.

Aggressiveness of Cephalosporium maydis causing late wilt of maize in Spain.

PubMed

García-Carneros, A B; Girón, I; Molinero-Ruiz, L

2012-01-01

Late wilt of maize, caused by the vascular and soilborne pathogen Cephalosporium maydis, was identified in the Iberian Peninsula in 2008. During the last years the incidence and economical impact of the disease has importantly increased both in Portugal and Spain. Varieties of maize displaying tolerance to the pathogen are available, but the effectiveness can be dependent on the virulence of the fungus (i.e. ability to cause disease on a specific genotype). On the other hand, strains of crop pathogens from different geographic origins can differ with regard to the degree of disease caused on a specific genotype (i.e. aggressiveness). Our working hypothesis was that isolates of C. maydis from different maize growing areas may differ in aggressiveness towards maize plants. Seven fungal strains were isolated in 2009 from diseased plants collected in the most important maize growing regions of Spain and used to inoculate two susceptible maize varieties grown in shadehouse from March to July 2010. The experimental unit consisted of two 4-day-old seedlings planted in an 8-liter pot filled with sand/silt previously infested with 200 g of wheat grains colonized by the fungi. Non colonized wheat grains were used for the control treatments. Six replications (pots) were established for each variety/isolate combination according to a complete randomized 2 x 8 factorial design. The percentage of necrotic and dry aboveground tissues was recorded 14 weeks after inoculation and thereafter weekly until physiological senescence of the control plants. At the end of the experiment, weights of roots and aboveground parts of the plants were recorded. Initial occurrence of symptoms in the plants was significantly dependent on the isolate of C. maydis and on the maize variety. However, final severity of aboveground symptoms (leaf necroses and drying up) was only dependent on the fungal isolate. All the isolates significantly reduced the root weight of both varieties of maize. The highest root weight reductions were also associated to a significant low weight of above-ground parts. Considering all the symptoms analysed and their progression in the maize plants, our results reveal that a diversity of aggressiveness exists among isolates of C. maydis. The need for a characterization of maize genotypes by their reaction against highly aggressive isolates of the fungus in the Iberian Peninsula is suggested. This study is a first step towards a recommendation of crop varieties that are tolerant to C. maydis in different areas of the Iberian Peninsula. Future research aims at studying the relationship between aggressiveness levels, molecular characteristics and geographical origin whithin C. maydis.

Characterization of cell death caused by diplodiatoxin and dipmatol, toxic metabolites of Stenocarpella maydis.

PubMed

Masango, Mxolisi G; Ellis, Charlotte E; Botha, Christo J

2015-08-01

Diplodiosis, a neuromycotoxicosis of cattle and sheep grazing on mouldy cobs infected by Stenocarpella maydis, is considered the last major veterinary mycotoxicosis for which the causative mycotoxin is still unknown. The current study was aimed at characterizing the cell death observed in mouse neuroblastoma (Neuro-2a), Chinese hamster ovary (CHO-K1) and Madin-Darby bovine kidney (MDBK) cell lines exposed to the S. maydis metabolites (i.e. diplodiatoxin and dipmatol) by investigating the roles of necrosis and apoptosis. Necrosis was investigated using the lactate dehydrogenase (LDH) leakage and propidium iodide (PI) flow cytometry assays and apoptosis was evaluated using the caspase-3/7 and Annexin V flow cytometry assays. In addition, transmission electron microscopy (TEM) was used to correlate the cell death pathways observed in this study with their typical morphologies. Both diplodiatoxin and dipmatol (750 μM) induced necrosis and caspase-dependent apoptosis in Neuro-2a, CHO-K1 and MDBK cells. Ultrastructurally, the two mycotoxins induced mitochondrial damage, cytoplasmic vacuolation and nuclear fragmentation in the three cell lines. These findings have laid a foundation for future studies aimed at elucidating in detail the mechanism of action of the S. maydis metabolites. Copyright © 2015 Elsevier Ltd. All rights reserved.

Actinomycin D Inhibition of the Zinc-induced Formation of Cytochrome c in Ustilago1

PubMed Central

Brown, D. H.; Cappellini, R. A.; Price, C. A.

1966-01-01

As reported earlier by Grimm & Allen, the addition of zinc to the sporidia of the smut fungus, Ustilago sphaerogena, evokes the formation of large amounts of cytochrome c. This occurs under conditions where the rates of increase of dry weight, RNA, and DNA remain unaffected. Actinomycin D added with zinc specifically abolishes the formation of cytochrome c. The system behaves as if cytochrome c were formed de novo. PMID:5956845

Reprint of "Sequence and phylogenetic analyses of novel totivirus-like double-stranded RNAs from field-collected powdery mildew fungi".

PubMed

Kondo, Hideki; Hisano, Sakae; Chiba, Sotaro; Maruyama, Kazuyuki; Andika, Ida Bagus; Toyoda, Kazuhiro; Fujimori, Fumihiro; Suzuki, Nobuhiro

2016-07-02

The identification of mycoviruses contributes greatly to understanding of the diversity and evolutionary aspects of viruses. Powdery mildew fungi are important and widely studied obligate phytopathogenic agents, but there has been no report on mycoviruses infecting these fungi. In this study, we used a deep sequencing approach to analyze the double-stranded RNA (dsRNA) segments isolated from field-collected samples of powdery mildew fungus-infected red clover plants in Japan. Database searches identified the presence of at least ten totivirus (genus Totivirus)-like sequences, termed red clover powdery mildew-associated totiviruses (RPaTVs). The majority of these sequences shared moderate amino acid sequence identity with each other (<44%) and with other known totiviruses (<59%). Nine of these identified sequences (RPaTV1a, 1b and 2-8) resembled the genome of the prototype totivirus, Saccharomyces cerevisiae virus-L-A (ScV-L-A) in that they contained two overlapping open reading frames (ORFs) encoding a putative coat protein (CP) and an RNA dependent RNA polymerase (RdRp), while one sequence (RPaTV9) showed similarity to another totivirus, Ustilago maydis virus H1 (UmV-H1) that encodes a single polyprotein (CP-RdRp fusion). Similar to yeast totiviruses, each ScV-L-A-like RPaTV contains a -1 ribosomal frameshift site downstream of a predicted pseudoknot structure in the overlapping region of these ORFs, suggesting that the RdRp is translated as a CP-RdRp fusion. Moreover, several ScV-L-A-like sequences were also found by searches of the transcriptome shotgun assembly (TSA) libraries from rust fungi, plants and insects. Phylogenetic analyses show that nine ScV-L-A-like RPaTVs along with ScV-L-A-like sequences derived from TSA libraries are clustered with most established members of the genus Totivirus, while one RPaTV forms a new distinct clade with UmV-H1, possibly establishing an additional genus in the family. Taken together, our results indicate the presence of diverse, novel totiviruses in the powdery mildew fungus populations infecting red clover plants in the field. Copyright © 2015 Elsevier B.V. All rights reserved.

Diplonine, a neurotoxin isolated from cultures of the fungus Stenocarpella maydis (Berk.) Sacc. that induces diplodiosis.

PubMed

Snyman, Leendert D; Kellerman, T Stephanus; Vleggaar, Robert; Flett, Bradley C; Basson, Karin M; Schultz, R Anitra

2011-08-24

Diplodiosis is a neuromycotoxicosis of cattle and sheep caused by ingestion of maize infected with the ear-rot fungus Stenocarpella (= Diplodia ) maydis . Apart from ataxia, paresis, and paralysis, the toxin is responsible for stillbirths and neonatal losses characterized by the presence of spongiform degeneration in the white matter of the brain in the offspring of dams exposed to infected maize cobs. In the present study a toxin, named diplonine, which induced neurological signs in guinea pigs resembling some of those occurring in cattle and sheep, was isolated from S. maydis cultures. Purification of diplonine was achieved by methanol extraction followed by chromatographic separation on silica gel and RP-18 stationary phases. The structure and relative configuration of diplonine were defined by analysis of NMR and MS data as (S)-2-amino-2-[(1R,2S)-1-hydroxy-2-methylcyclopropyl]acetic acid or the (S)-2-amino-2-[(1S,2R)-diastereomer.

Evaluation of corn germplasm lines for multiple ear-colonizing insect and disease resistance.

PubMed

Ni, Xinzhi; Xu, Wenwei; Blanco, Michael H; Wilson, Jeffrey P

2012-08-01

Ear-colonizing insects and diseases that reduce yield and impose health threats by mycotoxin contaminations in the grain, are critical impediments for corn (Zea mays L.) production in the southern United States. Ten germplasm lines from the Germplasm Enhancement of Maize (GEM) Program in Ames, IA, and Raleigh, NC, and 10 lines (derived from GEM germplasm) from the Texas Agricultural Experiment Station in Lubbock, TX, were examined in 2007 and 2008 with local resistant and susceptible controls. Four types of insect damage and smut disease (Ustilago maydis) infection, as well as gene X environment (G X E) interaction, was assessed on corn ears under field conditions. Insect damage on corn ears was further separated as cob and kernel damage. Cob penetration rating was used to assess corn earworm [Helicoverpa zea (Boddie)] and fall armyworm [Spodoptera frugiperda (J.E. Smith)] feeding on corn cobs, whereas kernel damage was assessed using three parameters: 1) percentage of kernels discolored by stink bugs (i.e., brown stink bug [Euschistus serous (Say)], southern green stink bug [Nezara viridula (L.)], and green stink bug [Chinavia (Acrosternum) hilare (Say)]; 2) percentage of maize weevil (Sitophilus zeamais Motschulsky)-damaged kernels; and 3) percentage of kernels damaged by sap beetle (Carpophilus spp.), "chocolate milkworm" (Moodna spp.), and pink scavenger caterpillar [Pyroderces (Anatrachyntis) rileyi (Walsingham)]. The smut infection rates on ears, tassels, and nodes also were assessed. Ear protection traits (i.e., husk tightness and extension) in relation to insect damage and smut infection also were examined. Significant differences in insect damage, smut infection, and husk protection traits were detected among the germplasm lines. Three of the 20 germplasm lines were identified as being multiple insect and smut resistant. Of the three lines, entries 5 and 7 were derived from DKXL370, which was developed using corn germplasm from Brazil, whereas entry 14 was derived from CUBA117.

The cultural significance of wild mushrooms in San Mateo Huexoyucan, Tlaxcala, Mexico

PubMed Central

2014-01-01

Background We performed an ethnomycological study in a community in Tlaxcala, Central Mexico to identify the most important species of wild mushrooms growing in an oak forest, their significance criteria, and to validate the Cultural Significance Index (CSI). Methods Thirty-three mestizo individuals were randomly selected in San Mateo Huexoyucan and were asked seven questions based on criteria established by the CSI. Among the 49 mushroom species collected in the oak forest and open areas, 20 species were mentioned most often and were analyzed in more detail. Ordination and grouping techniques were used to determine the relationship between the cultural significance of the mushroom species, according to a perceived abundance index, frequency of use index, taste score appreciation index, multifunctional food index, knowledge transmission index, and health index. Results The mushrooms with highest CSI values were Agaricus campestris, Ramaria spp., Amanita aff. basii, Russula spp., Ustilago maydis, and Boletus variipes. These species were characterized by their good taste and were considered very nutritional. The species with the lowest cultural significance included Russula mexicana, Lycoperdon perlatum, and Strobylomyces strobilaceus. The ordination and grouping analyses identified four groups of mushrooms by their significance to the people of Huexoyucan. The most important variables that explained the grouping were the taste score appreciation index, health index, the knowledge transmission index, and the frequency of use index. Conclusions A. aff. basii and A. campestris were the most significant wild mushrooms to the people of San Mateo. The diversity of the Russula species and the variety of Amanita and Ramaria species used by these people was outstanding. Environments outside the forest also produced useful resources. The CSI used in Oaxaca was useful for determining the cultural significance of mushrooms in SMH, Tlaxcala. This list of mushrooms can be used in conservation proposals for the Quercus forests in the area. PMID:24597704

Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust.

PubMed

Rochi, Lucia; Diéguez, María José; Burguener, Germán; Darino, Martín Alejandro; Pergolesi, María Fernanda; Ingala, Lorena Romina; Cuyeu, Alba Romina; Turjanski, Adrián; Kreff, Enrique Domingo; Sacco, Francisco

2018-03-01

Rust fungi are one of the most devastating pathogens of crop plants. The biotrophic fungus Puccinia sorghi Schwein (Ps) is responsible for maize common rust, an endemic disease of maize (Zea mays L.) in Argentina that causes significant yield losses in corn production. In spite of this, the Ps genomic sequence was not available. We used Illumina sequencing to rapidly produce the 99.6Mbdraft genome sequence of Ps race RO10H11247, derived from a single-uredinial isolate from infected maize leaves collected in the Argentine Corn Belt Region during 2010. High quality reads were obtained from 200bppaired-end and 5000bpmate-paired libraries and assembled in 15,722 scaffolds. A pipeline which combined an ab initio program with homology-based models and homology to in planta enriched ESTs from four cereal pathogenic fungus (the three sequenced wheat rusts and Ustilago maydis) was used to identify 21,087 putative coding sequences, of which 1599 might be part of the Ps RO10H11247 secretome. Among the 458 highly conserved protein families from the euKaryotic Orthologous Groups (KOG) that occur in a wide range of eukaryotic organisms, 97.5% have at least one member with high homology in the Ps assembly (TBlastN, E-value⩽e-10) covering more than 50% of the length of the KOG protein. Comparative studies with the three sequenced wheat rust fungus, and microsynteny analysis involving Puccinia striiformis f. sp. tritici (Pst, wheat stripe rust fungus), support the quality achieved. The results presented here show the effectiveness of the Illumina strategy for sequencing dikaryotic genomes of non-model organisms and provides reliable DNA sequence information for genomic studies, including pathogenic mechanisms of this maize fungus and molecular marker design. Copyright © 2016 Elsevier Inc. All rights reserved.

Incidence of Fusarium moniliforme Sheld. in Zea mays L. in the rainforest zone of Nigeria.

PubMed

Iloba, C

1979-01-01

45 seed samples from 7 states of the rainforest zone of Nigeria (Ogun, Ondo, Oyo, Bendel, Anambra, Imo, and Cross River) were screened for phytopathogen incidence. Whereas Drechslera maydis was found in 30 and Cephalosporium maydis in 79% of the samples were infected by Fusarium moniliforme, with 70% of the samples showing heavy infection. In view of the widespread nature of this economically important fungus on maize in the main cultivation area of Nigeria, the necessity for routine laboratory seed health tests is clearly indicated.

An ultrastructural study of Paraphysoderma sedebokerense (Blastocladiomycota), an epibiotic parasite of microalgae.

PubMed

Letcher, Peter M; Lee, Philip A; Lopez, Salvador; Burnett, Micheal; McBride, Robert C; Powell, Martha J

2016-03-01

Successful algal cultivation for biofuel production is one path in the transition to a renewable energy economy. The green alga Scenedesmus dimorphus is a candidate for biofuel production, but is subject to parasitism and subsequent population crash when cultivated in open ponds. From an open pond cultivating S. dimorphus for biofuel production in New Mexico, USA, an amoeboid parasite was isolated, designated as isolate FD61, and its rDNA operon sequenced. A BLAST search for nuc 18S rDNA (18S) sequence similarity identified the parasite as Paraphysoderma sedebokerense (Blastocladiomycota). Here, we examine the ultrastructure of P. sedebokerense and compare it with that of a sister taxon, Physoderma maydis. The parasite has thin-walled vegetative sporangia and thick-walled resting sporangia. Our observations indicate that amoeboid swarmers are produced in the vegetative phase, while either amoeboid swarmers or zoospores are the product of meiosis in resting sporangia. Meiosis is confirmed by the presence of synaptonemal complexes in resting sporangia nuclei. Notably, P. sedebokerense has a Golgi apparatus with stacked cisternae, a feature reported for P. maydis, but which is absent in all other examined taxa in Blastocladiomycota. This report furthers our knowledge of the life cycle of P. sedebokerense. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Clues to an evolutionary mystery: the genes for T-toxin, enabler of the devastating 1970 Southern Corn Leaf Blight epidemic, are present in ancestral species, suggesting an ancient origin.

PubMed

Condon, Bradford J; Elliott, Candace E; Gonzalez, Jonathan; Yun, Sung-Hwan; Akagi, Yasunori; Wiesner-Hanks, Tyr; Kodama, Motoichiro; Turgeon, Gillian

2018-05-24

The Southern Corn Leaf Blight epidemic of 1970 devastated fields of T-cytoplasm corn planted in monoculture throughout the eastern US. The epidemic was driven by race T, a previously unseen race of Cochliobolus heterostrophus. A second fungus, Phyllosticta zeae-maydis, with the same biological specificity, appeared coincidentally. Race T produces T-toxin, while P. zeae-maydis produces PM-toxin, both host selective polyketide toxins necessary for supervirulence. Present abundance of genome sequences offers an opportunity to tackle the evolutionary origins of T- and PM- toxin biosynthetic genes, previously thought unique to these species. Using the C. heterostrophus genes as probes, we identified orthologs in six additional Dothideomycete and three Eurotiomycete species. In stark contrast to the genetically fragmented race T Tox1 locus which encodes these genes, all newly found Tox1-like genes in other species reside at a single collinear locus. This compact arrangement, phylogenetic analyses, comparisons of Tox1 protein tree topology to a species tree, and Tox1 gene characteristics suggest that the locus is ancient and that some species, including C. heterostrophus, gained Tox1 by horizontal gene transfer. C. heterostrophus and P. zeae-maydis did not exchange Tox1 DNA at the time of the SCLB epidemic, but how they acquired Tox1 remains uncertain. The presence of additional genes in Tox1-like clusters of other species, but not in C. heterostrophus and P. zeae-maydis, suggests that the metabolites produced differ from T- and PM-toxin.

Genome sequence and virulence variation-related transcriptome profiles of Curvularia lunata, an important maize pathogenic fungus.

PubMed

Gao, Shigang; Li, Yaqian; Gao, Jinxin; Suo, Yujuan; Fu, Kehe; Li, Yingying; Chen, Jie

2014-07-24

Curvularia lunata is an important maize foliar fungal pathogen that distributes widely in maize growing area in China. Genome sequencing of the pathogen will provide important information for globally understanding its virulence mechanism. We report the genome sequences of a highly virulent C. lunata strain. Phylogenomic analysis indicates that C. lunata was evolved from Bipolaris maydis (Cochliobolus heterostrophus). The highly virulent strain has a high potential to evolve into other pathogenic stains based on analyses on transposases and repeat-induced point mutations. C. lunata has a smaller proportion of secreted proteins as well as B. maydis than entomopathogenic fungi. C. lunata and B. maydis have a similar proportion of protein-encoding genes highly homologous to experimentally proven pathogenic genes from pathogen-host interaction database. However, relative to B. maydis, C. lunata possesses not only many expanded protein families including MFS transporters, G-protein coupled receptors, protein kinases and proteases for transport, signal transduction or degradation, but also many contracted families including cytochrome P450, lipases, glycoside hydrolases and polyketide synthases for detoxification, hydrolysis or secondary metabolites biosynthesis, which are expected to be crucial for the fungal survival in varied stress environments. Comparative transcriptome analysis between a lowly virulent C. lunata strain and its virulence-increased variant induced by resistant host selection reveals that the virulence increase of the pathogen is related to pathways of toxin and melanin biosynthesis in stress environments, and that the two pathways probably have some overlaps. The data will facilitate a full revelation of pathogenic mechanism and a better understanding of virulence differentiation of C. lunata.

Indirect selection for resistance to ear rot and leaf diseases in maize lines using biplots.

PubMed

Pereira, G S; Camargos, R B; Balestre, M; Von Pinho, R G; C Melo, W M

2015-09-21

Leaf disease and ear rot have caused reductions in maize yield in Brazil and other producer countries. Therefore, the aims of this study were to analyze the association between husked ear yield and the severity of maize white spot, gray leaf spot, helminthosporium, and ear rot caused by Fusarium verticillioides and Diplodia maydis using biplots in a mixed-model approach. The responses of 238 lines introduced to Brazil and four controls were evaluated using an incomplete block design with three replicates in two locations: Lavras and Uberlândia, Minas Gerais, Brazil. Two experiments were conducted in each location, one with F. verticillioides and the other with D. maydis. The mixed models elucidated the relationship between yield, leaf disease, and ear disease. Significant genotype x environment and genotype x pathogen interactions were observed. In conclusion, husked ear yield is more associated with ear rot than with the leaf diseases evaluated, justifying the indirect selection for resistance to kernel rot in maize-F. verticillioides and maize-D. maydis pathosystems by yield evaluation.

Diuretic activity of Maydis stigma extract in rats.

PubMed

Maksimović, Z; Dobrić, S; Kovacević, N; Milovanović, Z

2004-12-01

Maydis stigma (corn silk) is a herbal drug reputed for the treatment of urinary ailments in various traditional medicine systems. To determine its influence on urinary volume and the excretion of sodium, potassium and chloride, 5% and 10% decoctions were administered daily to adult male Wistar rats for eight days. The concentration of electrolytes and urea in plasma, the influence of treatment on urinary pH value as well as creatinine clearance were also investigated. Daily oral administration of 5% decoction at the dose of 10 ml/kg led to a significant and acute diuresis in rats, reaching the peak value in the first 24 h of treatment. Over a similar period, application of 10% decoction did not affect urinary excretion of water, but significantly increased the pH value of excreted urine. A significant decrease in sodium and chloride plasma levels was observed in both treated groups. The creatinine clearance was markedly increased after the treatment with both extracts. Our findings indicate that the diuretic effect of 5% aqueous Maydis stigma extract is in accordance with the increase in glomerular filtration rate and inhibition of sodium and chloride tubular reabsorption, caused a by still unidentified intrinsic factor, but not the salt-loading effect.

Genome-Wide Annotation and Comparative Analysis of Cytochrome P450 Monooxygenases in Basidiomycete Biotrophic Plant Pathogens

PubMed Central

Sun, Yuxin; Letsimo, Elizabeth Mpholoseng; Parvez, Mohammad; Yu, Jae-Hyuk; Mashele, Samson Sitheni; Syed, Khajamohiddin

2015-01-01

Fungi are an exceptional source of diverse and novel cytochrome P450 monooxygenases (P450s), heme-thiolate proteins, with catalytic versatility. Agaricomycotina saprophytes have yielded most of the available information on basidiomycete P450s. This resulted in observing similar P450 family types in basidiomycetes with few differences in P450 families among Agaricomycotina saprophytes. The present study demonstrated the presence of unique P450 family patterns in basidiomycete biotrophic plant pathogens that could possibly have originated from the adaptation of these species to different ecological niches (host influence). Systematic analysis of P450s in basidiomycete biotrophic plant pathogens belonging to three different orders, Agaricomycotina (Armillaria mellea), Pucciniomycotina (Melampsora laricis-populina, M. lini, Mixia osmundae and Puccinia graminis) and Ustilaginomycotina (Ustilago maydis, Sporisorium reilianum and Tilletiaria anomala), revealed the presence of numerous putative P450s ranging from 267 (A. mellea) to 14 (M. osmundae). Analysis of P450 families revealed the presence of 41 new P450 families and 27 new P450 subfamilies in these biotrophic plant pathogens. Order-level comparison of P450 families between biotrophic plant pathogens revealed the presence of unique P450 family patterns in these organisms, possibly reflecting the characteristics of their order. Further comparison of P450 families with basidiomycete non-pathogens confirmed that biotrophic plant pathogens harbour the unique P450 families in their genomes. The CYP63, CYP5037, CYP5136, CYP5137 and CYP5341 P450 families were expanded in A. mellea when compared to other Agaricomycotina saprophytes and the CYP5221 and CYP5233 P450 families in P. graminis and M. laricis-populina. The present study revealed that expansion of these P450 families is due to paralogous evolution of member P450s. The presence of unique P450 families in these organisms serves as evidence of how a host/ecological niche can influence shaping the P450 content of an organism. The present study initiates our understanding of P450 family patterns in basidiomycete biotrophic plant pathogens. PMID:26536121

Amino Acid Permeases and Virulence in Cryptococcus neoformans

PubMed Central

Takahashi, Juliana Possato Fernandes; Guerra, Juliana Mariotti; Santos, Dayane Cristina da Silva; Purisco, Sônia Ueda; Melhem, Márcia de Souza Carvalho; Fazioli, Raquel dos Anjos; Phanord, Clerlune; Sartorelli, Patrícia; Vallim, Marcelo A.

2016-01-01

Fungal opportunistic pathogens colonize various environments, from plants and wood to human and animal tissue. Regarding human pathogens, one great challenge during contrasting niche occupation is the adaptation to different conditions, such as temperature, osmolarity, salinity, pressure, oxidative stress and nutritional availability, which may constitute sources of stress that need to be tolerated and overcome. As an opportunistic pathogen, C. neoformans faces exactly these situations during the transition from the environment to the human host, encountering nutritional constraints. Our previous and current research on amino acid biosynthetic pathways indicates that amino acid permeases are regulated by the presence of the amino acids, nitrogen and temperature. Saccharomyces cerevisiae and Candida albicans have twenty-four and twenty-seven genes encoding amino acid permeases, respectively; conversely, they are scarce in number in Basidiomycetes (C. neoformans, Coprinopsis cinerea and Ustilago maydis), where nine to ten permease genes can be found depending on the species. In this study, we have demonstrated that two amino acid permeases are essential for virulence in C. neoformans. Our data showed that C. neoformans uses two global and redundant amino acid permeases, Aap4 and Aap5 to respond correctly to thermal and oxidative stress. Double deletion of these permeases causes growth arrest in C. neoformans at 37°C and in the presence of hydrogen peroxide. The inability to uptake amino acid at a higher temperature and under oxidative stress also led to virulence attenuation in vivo. Our data showed that thermosensitivity caused by the lack of permeases Aap4 and Aap5 can be remedied by alkaline conditions (higher pH) and salinity. Permeases Aap4 and Aap5 are also required during fluconazole stress and they are the target of the plant secondary metabolite eugenol, a potent antifungal inhibitor that targets amino acid permeases. In summary, our work unravels (i) interesting physiological property of C. neoformans regarding its amino acid uptake system; (ii) an important aspect of virulence, which is the need for amino acid permeases during thermal and oxidative stress resistance and, hence, host invasion and colonization; and (iii) provides a convenient prototype for antifungal development, which are the amino acid permeases Aap4/Aap5 and their inhibitor. PMID:27695080

Use of HPLC for the detection of iron chelators in cultures of bacteria, fungi, and algae. [E. coli; Bacillus megaterium; Ustilago sphaerogena; Anabaena flos-aqua

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

Boyer, G.L.; Speirs, R.J.; Morse, P.D.

1990-06-01

Iron is essential for the growth of living cells. To meet biochemical needs, microorganisms, including algae, produce high affinity chelators termed siderophores. These compounds solubilize Fe and increase its bioavailability. We have developed a new method to study siderophore formation in cultured and natural environments. Based on the fact siderophores tightly bind 55-Fe, the radioactive complexes can be separated by HPLC using an inert PRP-1 column and detected by scintillation counting. This method cleanly resolves several known siderophores, including ferrichrome A, ferrichrome, desferal, and rhodotorulic acid. The optimization of the method and its use for analysis of siderophore formation inmore » bacteria (E. coli, and Bacillus megaterium), fungi (Ustilago sphaerogena), and cyanobacteria (Anabaena flos-aqua UTEX 1444 and Anabaena sp. ATCC 27898) will be presented.« less

Corn silk (Stigma maydis) in healthcare: a phytochemical and pharmacological review.

PubMed

Hasanudin, Khairunnisa; Hashim, Puziah; Mustafa, Shuhaimi

2012-08-13

Corn silk (Stigma maydis) is an important herb used traditionally by the Chinese, and Native Americans to treat many diseases. It is also used as traditional medicine in many parts of the world such as Turkey, United States and France. Its potential antioxidant and healthcare applications as diuretic agent, in hyperglycemia reduction, as anti-depressant and anti-fatigue use have been claimed in several reports. Other uses of corn silk include teas and supplements to treat urinary related problems. The potential use is very much related to its properties and mechanism of action of its plant's bioactive constituents such as flavonoids and terpenoids. As such, this review will cover the research findings on the potential applications of corn silk in healthcare which include its phytochemical and pharmacological activities. In addition, the botanical description and its toxicological studies are also included.

Zea mays, Stigma maydis prevents and extenuates acetaminophen-perturbed oxidative onslaughts in rat hepatocytes.

PubMed

Saheed, Sabiu; Frans Hendrik, O'Neill; Tom, Ashafa Anofi Omotayo

2016-11-01

Zea mays L. (Poaceae) Stigma maydis is an underutilized product of corn cultivation finding therapeutic applications in oxidative stress-related disorders. This study investigated its aqueous extract against acetaminophen (APAP)-perturbed oxidative insults in rat hepatocytes. Hepatotoxic rats were orally pre- and post-treated with the extract (at 200 and 400 mg/kg body weight) and vitamin C (200 mg/kg body weight), respectively, for 14 days. Liver function, antioxidative and histological analyses were thereafter evaluated. The APAP-induced marked (p < 0.05) increases in the activities of alkaline phosphatase, alanine aminotransferase, aspartate aminotransferase, gamma glutamyl transferase and the concentrations of bilirubin, oxidized glutathione, protein carbonyls, malondialdehyde, conjugated dienes, lipid hydroperoxides and fragmented DNA were dose-dependently extenuated in the extract-treated animals. The extract also significantly (p < 0.05) improved the reduced activities of superoxide dismutase, catalase, glutathione reductase and glutathione peroxidase as well as total protein, albumin and glutathione concentrations in the hepatotoxic rats. These improvements may be attributed to the bioactive constituents as revealed by the gas chromatography-mass spectrometric chromatogram of the extract. The observed effects compared favourably with vitamin C and are informative of hepatoprotective and antioxidative attributes of the extract and were further supported by the histological analysis. The data from the present findings suggest that Stigma maydis aqueous extract is capable of preventing and ameliorating APAP-mediated oxidative hepatic damage via enhancement of antioxidant defence systems.

Differential activity staining: its use in characterization of guanylyl-specific ribonuclease in the genus Ustilago.

PubMed Central

Blank, A; Dekker, C A

1975-01-01

Guanylyl-specific ribonuclease can be identified by a novel technique employing electrophoresis in polyacrylamide slabs followed by differential activity staining. The technique requires as little as 7 ng of enzyme which may be grossly admixed with contaminants, including other ribonucleases. Upon electrophoresis and activity staining, a variety of ribonucleases can be visualized as light or clear bands in a colored background formed by toluidine blue complexed with oligonucleotide substrate. Guanylyl-specific ribonuclease, which is detectable when using an oligonucleotide substrate of random base sequence, does not yield a band when using oligonucleotides bearing guanylyl residues at the 3'-termini only and containing, therefore, no susceptible internucleotide bonds; in contrast, a ribonuclease with a different base specificity or no base specificity yields a band with either substrate. This differential activity staining method for establishing guanylyl specificity permits estimation of the extent of nonspecific cleavage of internucleotide linkages by a putatively guanylyl-specific enzyme and is at least as sensitive as conventional procedures for determination of base specificity. With this new technique guanyloribonuclease has been identified in the unfractionated culture medium of 10 organisms belonging to the phytopathogenic fungal genus Ustilago. It is suggested that guanylyl-specific ribonuclease is widely distributed among Ustilago species; its electrophoretic properties may be revealing of phylogenetic relationships among these plant parasites and among their hosts. The general technique of differential activity staining, developed for determination of the base specificity of ribonucleases, may be widely applicable to analysis of enzymes catalyzing depolymerization reactions. Images PMID:813217

Influence of light on the biosynthesis of ophiobolin A by Bipolaris maydis.

PubMed

Fanelli, Francesca; Reveglia, Pierluigi; Masi, Marco; Mulè, Giuseppina; Zonno, Maria Chiara; Cimmino, Alessio; Vurro, Maurizio; Evidente, Antonio

2017-04-01

Ophiobolin A (O-A) is a sesterpenoid with numerous biological activities, including potential anticancer effects. Its production at an industrial level is hampered due to inability of fungus Bipolaris maydis to biosynthesise it in vitro in large amount. Among the environmental factors regulating fungal metabolism, light plays a crucial role. In this study, the use of different light wavelength (light emitting diodes (LEDs)) was evaluated to increase the O-A production. The white light allowed the highest production of the metabolite. The blue and green lights showed an inhibitory effect, reducing the production to 50%, as well as red and yellow but at a lower level. No correlation between fungal growth and metabolite production was found in relation to the light type. A novel application of LED technologies, which can be optimised to foster specific pathways and promote the production of metabolites having scientific and industrial interest was proposed.

Species of Cercospora associated with grey leaf spot of maize

PubMed Central

Crous, Pedro W.; Groenewald, Johannes Z.; Groenewald, Marizeth; Caldwell, Pat; Braun, Uwe; Harrington, Thomas C.

2006-01-01

Grey leaf spot is a serious yield-reducing disease of maize (Zea mays) in many parts of the world where this crop is cultivated. The causal organism associated with the disease is Cercospora zeae-maydis. Two potential sibling species have been recognized as Groups I and II. The DNA sequences for the internal transcribed spacers (ITS1 & ITS2), the 5.8S rRNA gene, elongation factor 1-α, histone H3, actin and calmodulin gene regions suggest that Groups I and II are two distinct species. Furthermore, Cercospora zeae-maydis (Group I) can be distinguished from C. zeina sp. nov. (Group II) by its faster growth rate on artificial media, the ability to produce cercosporin, longer conidiophores, and broadly fusiform conidia. A PCR-based test that distinguishes the two species was developed using species-specific primers designed from the histone H3 gene. PMID:18490979

Polyphenol contents and antioxidant activity of Maydis stigma extracts.

PubMed

Maksimović, Zoran; Malencić, Dorde; Kovacević, Nada

2005-05-01

The antioxidant activity and contents of various polyphenol classes in the silks of fifteen maize hybrids with economic importance in Serbia were evaluated. Total polyphenols, tannins and proanthocyanidins were determined spectrophotometrically, after extraction of plant material with 70% aqueous acetone under sonication at room temperature. In addition, flavonoid content was determined. Antioxidant activity of aqueous acetone extracts was evaluated by FRAP assay. A positive linear correlation between antioxidant activity and contents of all investigated polyphenol classes was established. The highest antioxidant activity was observed in the extract of NS 640 hybrid, which had high levels of all polyphenol classes examined. Results suggested strongly that polyphenol content should be considered as an important feature of the herbal drug Maydis stigma. For that reason, the biological source of this herbal drug needs to be more precisely defined, as observed activities and polyphenol contents were greatly dependent on plant material source.

The effect of some organic substances on the mycelium of the fungus Ustilago nuda (Jens.) Rostr.

PubMed

Krátká, J

1976-01-01

Research was performed for studying the effect of some organic compounds, considered by many authors as the products ob barley seed metabolism generated after anaerobic seed treatment, on the mycelium of the fungus Ustilago nuda (Jens.) Rostr. The author examined the effectiveness of ethylacohol, acetaldehyde, acetic acid, succinic acid, lactic acid, and hydroquinone in concentrations from 1 M to 10(-6) M, and the effectiveness of extracts from disinfected seeds in doses from 10 g to 0.001 g/l. The effect of the mentioned solutions was examined as exerted on the growth of dicaryotic mycelium and on the growth of the haploid promycelium of the fungus. The dicaryotic mycelium of Ustilago nuda (Jens.) Rostr. was cultivated on potato agar with benzoic acid. The presence of the acid prevents mitosis, and the chlamydospores germinate on the nutritive medium with two fibres having binuclear cells. The haploid promycelium was cultivated on potato agar; chlamydospores germinated with one four-cell fibre, and individual cells are mononuclear and haploid. Only later, a dicarytic mycelium is created in a complex process. In all the substances used, the concentration of 1 M was found to stop further growth of mycelium. The concentration of 10(-1) M of acetic acid and hydroquinone also stopped growth, the same concentration of acetaldehyde, lactic acid, succinic acid, ethylacohol stimulated mycelium growth in comparison with the control. The concentration of 10(-6) M stimulated mycelium growth in a majority of cases. Extracts from disinfected seeds did not influence mycelium growth significantly in all cases in comparison with the control. The results were similar in the two types of mycelium.

A complete toolset for the study of Ustilago bromivora and Brachypodium sp. as a fungal-temperate grass pathosystem

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

Rabe, Franziska; Bosch, Jason; Stirnberg, Alexandra

Due to their economic relevance, the study of plant pathogen interactions is of importance. However, elucidating these interactions and their underlying molecular mechanisms remains challenging since both host and pathogen need to be fully genetically accessible organisms. Here we present milestones in the establishment of a new biotrophic model pathosystem: Ustilago bromivora and Brachypodium sp. We provide a complete toolset, including an annotated fungal genome and methods for genetic manipulation of the fungus and its host plant. This toolset will enable researchers to easily study biotrophic interactions at the molecular level on both the pathogen and the host side. Moreover,more » our research on the fungal life cycle revealed a mating type bias phenomenon. U. bromivora harbors a haplo-lethal allele that is linked to one mating type region. As a result, the identified mating type bias strongly promotes inbreeding, which we consider to be a potential speciation driver.« less

A complete toolset for the study of Ustilago bromivora and Brachypodium sp. as a fungal-temperate grass pathosystem

DOE PAGES

Rabe, Franziska; Bosch, Jason; Stirnberg, Alexandra; ...

2016-11-11

Due to their economic relevance, the study of plant pathogen interactions is of importance. However, elucidating these interactions and their underlying molecular mechanisms remains challenging since both host and pathogen need to be fully genetically accessible organisms. Here we present milestones in the establishment of a new biotrophic model pathosystem: Ustilago bromivora and Brachypodium sp. We provide a complete toolset, including an annotated fungal genome and methods for genetic manipulation of the fungus and its host plant. This toolset will enable researchers to easily study biotrophic interactions at the molecular level on both the pathogen and the host side. Moreover,more » our research on the fungal life cycle revealed a mating type bias phenomenon. U. bromivora harbors a haplo-lethal allele that is linked to one mating type region. As a result, the identified mating type bias strongly promotes inbreeding, which we consider to be a potential speciation driver.« less

A complete toolset for the study of Ustilago bromivora and Brachypodium sp. as a fungal-temperate grass pathosystem

PubMed Central

Rabe, Franziska; Bosch, Jason; Stirnberg, Alexandra; Guse, Tilo; Bauer, Lisa; Seitner, Denise; Rabanal, Fernando A; Czedik-Eysenberg, Angelika; Uhse, Simon; Bindics, Janos; Genenncher, Bianca; Navarrete, Fernando; Kellner, Ronny; Ekker, Heinz; Kumlehn, Jochen; Vogel, John P; Gordon, Sean P; Marcel, Thierry C; Münsterkötter, Martin; Walter, Mathias C; Sieber, Christian MK; Mannhaupt, Gertrud; Güldener, Ulrich; Kahmann, Regine; Djamei, Armin

2016-01-01

Due to their economic relevance, the study of plant pathogen interactions is of importance. However, elucidating these interactions and their underlying molecular mechanisms remains challenging since both host and pathogen need to be fully genetically accessible organisms. Here we present milestones in the establishment of a new biotrophic model pathosystem: Ustilago bromivora and Brachypodium sp. We provide a complete toolset, including an annotated fungal genome and methods for genetic manipulation of the fungus and its host plant. This toolset will enable researchers to easily study biotrophic interactions at the molecular level on both the pathogen and the host side. Moreover, our research on the fungal life cycle revealed a mating type bias phenomenon. U. bromivora harbors a haplo-lethal allele that is linked to one mating type region. As a result, the identified mating type bias strongly promotes inbreeding, which we consider to be a potential speciation driver. DOI: http://dx.doi.org/10.7554/eLife.20522.001 PMID:27835569

The effect of meteorological factors on the daily variation of airborne fungal spores in Granada (southern Spain)

NASA Astrophysics Data System (ADS)

Sabariego, S.; Díaz de la Guardia, C.; Alba, F.

A study was made of the link between climatic factors and the daily content of certain fungal spores in the atmosphere of the city of Granada in 1994. Sampling was carried out with a Burkard 7-day-recording spore trap. The spores analysed corresponded to the taxa Alternaria, Ustilago and Cladosporium, with two morphologically different spore types in the latter genus, cladosporioides and herbarum. These spores were selected both for their allergenic capacity and for the high level of their presence in the atmosphere, particularly during the spring and autumn. The spores of Cladosporium were the most abundant (93.82% of the total spores identified). The Spearman correlation coefficients between the spore concentrations studied and the meteorological parameters show different indices depending on the taxon being analysed. Alternaria and Cladosporium are significantly correlated with temperature and hours of sunlight, while Ustilago shows positive correlation indices with relative humidity and negative indices with wind speed.

Systemic fungicidal activity of 1,4-oxathiin derivatives.

PubMed

Schmeling, B V; Kulka, M

1966-04-29

Treatment of pinto bean and barley seed with 1,4-oxathiin derivatives gave disease control by systemic fungicidal action of such pathogenic fungi as Uromyces phaseoli and Ustilago nuda. The two chemicals, D735 and F461, were highly specific and selective against the pathogens without injury of the hosts.

Stripe smuts of grasses: one lineage or high levels of polyphyly?

USDA-ARS?s Scientific Manuscript database

Stripe smut of grasses, Ustilago striiformis s.l., is caused by a complex of smut fungi widely distributed over temperate and subtropical regions. The disease results in the shredding and death of leaf tissue following the rupture of elongated sori. Nearly 100 different grass species in more than 30...

Genetics of Ustilago violacea. I. Carotenoid mutants and carotenogenesis

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

Garber, E.D.; Baird, M.L.; Chapman, D.J.

1975-12-01

Wild-type strains of Ustilago violacea produce pink colonies on laboratory medium and yield white, orange, pumpkin, and yellow colonies after uv mutagenesis. The wild-type strains contain neurosporene and lycopene; one orange mutant, $gamma$-carotene; and one yellow mutant, $beta$-carotene. One white mutant had no detectable carotenoids. Diploid colonies heterozygous for wild type and orange, pumpkin, yellow, or white are phenotypically wild type. Diploid colonies heterozygous for yellow and orange are also phenotypically wild type. Diploid colonies heterozygous for white and orange; white and yellow; and white, yellow, and orange are phenotypically light orange, light yellow, and orange- yellow, respectively. The whitemore » mutants give a circular complementation map; the color mutants fit a linear complementation map. We propose a multienzyme of four identical dehydrogenases and one or two identical cyclases for carotenogenesis in this species. The white and color mutants represent structural mutations altering the conformation of the dehydrogenase or cyclase, respectively. Furthermore, cyclases may or may not aggregate in association with the dehydrogenase aggregate to form the multienzyme aggregate responsible for the color mutants. (auth)« less

Diplodiatoxin, chaetoglobosins, and diplonine associated with a field outbreak of Stenocarpella ear rot in Illinois

USDA-ARS?s Scientific Manuscript database

Stenocarpella maydis causes a fungal dry-rot of maize ears and is associated with diplodiosis, a neuromycotoxicosis in cattle grazing harvested maize fields in southern Africa and Argentina. There have been no reports of Stenocarpella metabolites in maize crop residues. Chemical investigations of S....

Influence of Stenocarpella maydis infected corn on the dry grind ethanol process

USDA-ARS?s Scientific Manuscript database

Widespread epidemics of Stenocarpella ear rot (formerly Diplodia ear rot) have occurred throughout the central U.S. Corn Belt in recent years with reports of some fields containing more than 50% mummified ears. Ears infected within two weeks of silking may be completely mummified with white to grayi...

Influence of Stenocarpella maydis infected corn on the dry grind ethanol process

USDA-ARS?s Scientific Manuscript database

Widespread epidemics of Stenocarpella ear rot (formerly Diplodia ear rot) have occurred throughout the central U.S. Corn Belt in recent years with reports of some fields containing more than 50% mummified ears. Ears infected within two weeks of silking may be completely mummified with white to gray...

Isolation of Bacteria with Antifungal Activity against the Phytopathogenic Fungi Stenocarpella maydis and Stenocarpella macrospora

PubMed Central

Petatán-Sagahón, Iván; Anducho-Reyes, Miguel Angel; Silva-Rojas, Hilda Victoria; Arana-Cuenca, Ainhoa; Tellez-Jurado, Alejandro; Cárdenas-Álvarez, Isabel Oyuki; Mercado-Flores, Yuridia

2011-01-01

Stenocarpella maydis and Stenocarpella macrospora are the causal agents of ear rot in corn, which is one of the most destructive diseases in this crop worldwide. These fungi are important mycotoxin producers that cause different pathologies in farmed animals and represent an important risk for humans. In this work, 160 strains were isolated from soil of corn crops of which 10 showed antifungal activity against these phytopathogens, which, were identified as: Bacillus subtilis, Pseudomonas spp., Pseudomonas fluorescens, and Pantoea agglomerans by sequencing of 16S rRNA gene and the phylogenetic analysis. From cultures of each strain, extracellular filtrates were obtained and assayed to determine antifungal activity. The best filtrates were obtained in the stationary phase of B. subtilis cultures that were stable to the temperature and extreme pH values; in addition they did not show a cytotoxicity effect against brine shrimp and inhibited germination of conidia. The bacteria described in this work have the potential to be used in the control of white ear rot disease. PMID:22016606

Depolarization of the Electrogenic Transmembrane Electropotential of Zea mays L. by Bipolaris (Helminthosporium) maydis Race T Toxin, Azide, Cyanide, Dodecyl Succinic Acid, or Cold Temperature 1

PubMed Central

Mertz, Stuart M.; Arntzen, Charles J.

1978-01-01

The transmembrane electrical potential of root cells of Zea mays L. cv. W64A in a modified 1× Higinbotham solution was partially depolarized by semipurified toxin obtained from Bipolaris (Helminthosporium) maydis race T. At a given toxin concentration depolarization of Texas cytoplasm cells was much greater than for normal cytoplasm cells. This observation correlated directly to the differential host susceptibility to the fungus. The time course and magnitude of depolarization were dependent on toxin concentration; at high concentration the electropotential difference change was rapid. Cortex cells depolarized more slowly than epidermal cells indicating that the toxin slowly permeated intercellular regions. Toxin concentrations which affected electropotential difference were of the same magnitude as those required to inhibit root growth, ion uptake, and mitochondrial processes. Azide, cyanide, and cold temperature (5 C) gave the same partial depolarization as did the toxin. Dodecyl succinic acid caused complete depolarization. These and other data indicate that one of the primary actions of the toxin is to inhibit electrogenic ion pumps in the plasmalemma. PMID:16660605

Inheritance of Carboxin Resistance in a European Field Isolate of Ustilago nuda.

PubMed

Newcombe, G; Thomas, P L

2000-02-01

ABSTRACT Two carboxin-resistant field isolates of Ustilago nuda from Europe were crossed with a carboxin-sensitive field isolate from North America. Meiotic tetrads isolated from germinating F(1) teliospores of one of the hybrids were tested for carboxin resistance and mating type. Carboxin resistance was shown to be controlled by a single gene (CBX1R), because a 1:1 segregation of carboxin resistance was observed in all 27 tetrads. Tetrad analysis indicated that the loci for carboxin resistance (Cbx1) and mating type (MAT1) segregate independently but may be located on the same chromosome. Tetrad analysis was not possible with the F(1) hybrid of he other field isolate, and its resistance cannot yet be attributed to CBX1R. Carboxin resistance was qualitatively dominant to sensitivity in vitro, as demonstrated by triad analysis of germinating F(1) teliospores. Quantitative in planta infection percents supported the conclusion that CBX1R is dominant, although incompletely, in the F(1) hybrid of one of the field isolates. Also, fewer than expected carboxin-sensitive F(2) individuals were observed in planta. However, inoculations of host plants with U. nuda have resulted in similar, unexpected variation in the past.

Identification of alleles conferring resistance to gray leaf spot in maize derived from its wild progenitor species teosinte (Zea mays ssp. parviglumis)

USDA-ARS?s Scientific Manuscript database

Gray Leaf Spot [(GLS), causal agent Cercospora zeae-maydis and Cercospora zeina] is an important maize disease in the United States. Current control methods for GLS include using resistant cultivars, crop rotation, chemical applications, and conventional tillage to reduce inoculum levels. Teosinte ...

Influence of Stenocarpella maydis infected corn on the composition of corn kernel and its conversion into ethanol

USDA-ARS?s Scientific Manuscript database

Stenocarpella ear rot (formerly Diplodia ear rot) is resurfacing as a concern in the central United States Corn Belt. There are reports of some fields containing more than 50% mummified ears. Ears infected within two weeks of silking may be completely mummified with white to grayish brown mycelium c...

Identification of a chitinase modifying protein from Fusarium verticillioides: truncation of a host resistance protein by a fungalysin metalloprotease

USDA-ARS?s Scientific Manuscript database

Chitinase modifying proteins (cmps) are proteases, secreted by fungal pathogens, which truncate the plant class IV chitinases ChitA and ChitB during maize ear rot. Cmp activity has been characterized for Bipolaris zeicola and Stenocarpella maydis, but the identities of the proteases are not known. H...

Cloning and identification of Fv-cmp, a protease from Fusarium verticillioides that truncates Zea mays and Arabidopsis thaliana class IV chitinases

USDA-ARS?s Scientific Manuscript database

Chitinase modifying proteins (cmps) are proteases, secreted by fungal pathogens, that were originally identified as proteins that truncate class IV chitinases of maize during ear rot. Cmps from Bipolaris zeicola and Stenocarpella maydis have been characterized, but the identities of the proteases h...

Cytological study of radiation induced alterations in cytoplasmic factors controlling male sterility in corn. Progress report, February 28, 1973--December 1, 1973

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

Edwardson, J.R.

1973-01-01

Cytoplasmic male sterile accessions, other than T-type, are being backcrossed to adapted maintainer and restorer inbred corn lines. Fertile selections from gamma -irradiated T-type corn continue to exhibit resistance to infection by race-T of Helminthosporium maydis in field and greenhouse tests. Cytological comparisons of these fertile selections and T-sterile, maintainer, and restorer lines are continuing. Dominant male sterility and its suppression in S-cytoplasm corn is being investigated. lnduction of cytoplasmic male sterility in normal cytoplasm corn and suppression of susceptibility to Helminthosporium maydis infection in T cytoplasm corn is being attempted with chemical mutagens. Consistent differences in cytoplasmic inclusions inmore » sterile and maintainer Vicia faba were observed. Consistent differences in mitochondria were observed in cytological comparisons of normal and sterile corn. These abnormal mitochondria and non-Mendelian plastid abnormalities in corn, sorghum, tobacco, and petunia will be used in studying the fertilization process. Investigations of the properties of Datura Q-virus are near completion. Cytological and serological studies indicate the Q-virus is a strain of tobacco streak virus. Graft-transmission of cytoplasmic male sterility is being attempted in sunflower. (auth)« less

JPRS Report, Science and Technology USSR: Life Sciences.

DTIC Science & Technology

1990-09-26

newly observed smut flowers infected with Ustilago vaillantii smut, infection parasite does not destroy the host, so it probably does of its spores by...designed to further expand studies on transgenic plants. selected on hygromycin B. All characterized clones syn- pABDI was constructed from Escherichia coli...they numbered more than 2,000 in July- farms into four groups, according to number of workers: September. In livestock breeding , the largest number of

Toxicological evaluations of Stigma maydis (corn silk) aqueous extract on hematological and lipid parameters in Wistar rats.

PubMed

Saheed, Sabiu; Oladipipo, Ajani E; Abdulazeez, Abubakar A; Olarewaju, Sulyman A; Ismaila, Nurain O; Emmanuel, Irondi A; Fatimah, Quadri D; Aisha, Abubakar Y

2015-01-01

Despite the acclaimed phytotherapeutic attributes of Stigma maydis in folkloric medicine, there is paucity of information on its toxicity profile on hematological and lipid parameters. The toxicological effect of aqueous extract of corn silk at 100, 200 and 400 mg/kg body weight on hematological indices in Wistar rats were evaluated progressively at 24 h after 1, 7, 14, 21 and 28 days. Lipid parameters were also analyzed at the end of the experimental period. We observed that the extract did not exhibit any significant ( p  > 0.05) effect on red blood cells, hematocrit, hemoglobin, mean corpuscular volume, mean corpuscular hemoglobin, mean corpuscular hemoglobin concentration, and mean platelet volume at all the tested doses. The study however showed a significant increase in the serum levels of white blood cell, platelet, lymphocytes, high-density lipoprotein cholesterol; as well as feeding pattern in the animals, while the concentrations of total cholesterol, low-density lipoprotein cholesterol, and artherogenic index value were significantly lowered. These findings are suggestive of non-hematotoxic potential of the extract. Overall, the effect exhibited by corn silk extract in this study proved that, it is unlikely to be hematotoxic and could be a good candidature in the management of coronary heart diseases if consumed at the doses investigated.

Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

PubMed Central

2011-01-01

Background Rust fungi are biotrophic basidiomycete plant pathogens that cause major diseases on plants and trees world-wide, affecting agriculture and forestry. Their biotrophic nature precludes many established molecular genetic manipulations and lines of research. The generation of genomic resources for these microbes is leading to novel insights into biology such as interactions with the hosts and guiding directions for breakthrough research in plant pathology. Results To support gene discovery and gene model verification in the genome of the wheat leaf rust fungus, Puccinia triticina (Pt), we have generated Expressed Sequence Tags (ESTs) by sampling several life cycle stages. We focused on several spore stages and isolated haustorial structures from infected wheat, generating 17,684 ESTs. We produced sequences from both the sexual (pycniospores, aeciospores and teliospores) and asexual (germinated urediniospores) stages of the life cycle. From pycniospores and aeciospores, produced by infecting the alternate host, meadow rue (Thalictrum speciosissimum), 4,869 and 1,292 reads were generated, respectively. We generated 3,703 ESTs from teliospores produced on the senescent primary wheat host. Finally, we generated 6,817 reads from haustoria isolated from infected wheat as well as 1,003 sequences from germinated urediniospores. Along with 25,558 previously generated ESTs, we compiled a database of 13,328 non-redundant sequences (4,506 singlets and 8,822 contigs). Fungal genes were predicted using the EST version of the self-training GeneMarkS algorithm. To refine the EST database, we compared EST sequences by BLASTN to a set of 454 pyrosequencing-generated contigs and Sanger BAC-end sequences derived both from the Pt genome, and to ESTs and genome reads from wheat. A collection of 6,308 fungal genes was identified and compared to sequences of the cereal rusts, Puccinia graminis f. sp. tritici (Pgt) and stripe rust, P. striiformis f. sp. tritici (Pst), and poplar leaf rust Melampsora species, and the corn smut fungus, Ustilago maydis (Um). While extensive homologies were found, many genes appeared novel and species-specific; over 40% of genes did not match any known sequence in existing databases. Focusing on spore stages, direct comparison to Um identified potential functional homologs, possibly allowing heterologous functional analysis in that model fungus. Many potentially secreted protein genes were identified by similarity searches against genes and proteins of Pgt and Melampsora spp., revealing apparent orthologs. Conclusions The current set of Pt unigenes contributes to gene discovery in this major cereal pathogen and will be invaluable for gene model verification in the genome sequence. PMID:21435244

Antifungal Activity of a Phytoterpenoid (AOS-A) Isolated from Artabotrytis odoratissimus on Spore Germination of Some Fungi

PubMed Central

Singh, D. K.; Basha, S. Ameer; Sarma, B. K.; Pandey, V. B.

2006-01-01

Phytoterpenoid isolated from Artabotrytis odoratissimus inhibited spore germination of some plant pathogenic as well as saprophytic fungi e.g. Alternaria alternata, A. solani, Cercospora sp., Curvularia maculans, C. pennisetti, Fusarium udum, Helminthosporium echinochlova, H. frumentacie, H. penniseti and Ustilago cynodontis. In Curvularia maculans and H. frumentacie, spore germination was completely inhibited at 2000 ppm. However, Curvularia maculans and C. pennisetti showed considerable sensitivity to this chemical even at 500 ppm. PMID:24039483

Membrane Stabilization and Detoxification of Acetaminophen-Mediated Oxidative Onslaughts in the Kidneys of Wistar Rats by Standardized Fraction of Zea mays L. (Poaceae), Stigma maydis.

PubMed

Sabiu, S; O'Neill, F H; Ashafa, A O T

2016-01-01

This study evaluated membrane stabilization and detoxification potential of ethyl acetate fraction of Zea mays L., Stigma maydis in acetaminophen-induced oxidative onslaughts in the kidneys of Wistar rats. Nephrotoxic rats were orally pre- and posttreated with the fraction and vitamin C for 14 days. Kidney function, antioxidative and histological analyses were thereafter evaluated. The acetaminophen-mediated significant elevations in the serum concentrations of creatinine, urea, uric acid, sodium, potassium, and tissue levels of oxidized glutathione, protein-oxidized products, lipid peroxidized products, and fragmented DNA were dose-dependently assuaged in the fraction-treated animals. The fraction also markedly improved creatinine clearance rate, glutathione, and calcium concentrations as well as activities of superoxide dismutase, catalase, glutathione reductase, and glutathione peroxidase in the nephrotoxic rats. These improvements may be attributed to the antioxidative and membrane stabilization activities of the fraction. The observed effects compared favorably with that of vitamin C and are informative of the fraction's ability to prevent progression of renal pathological conditions and preserve kidney functions as evidently supported by the histological analysis. Although the effects were prominently exhibited in the fraction-pretreated groups, the overall data from the present findings suggest that the fraction could prevent or extenuate acetaminophen-mediated oxidative renal damage via fortification of antioxidant defense mechanisms.

Membrane Stabilization and Detoxification of Acetaminophen-Mediated Oxidative Onslaughts in the Kidneys of Wistar Rats by Standardized Fraction of Zea mays L. (Poaceae), Stigma maydis

PubMed Central

Sabiu, S.; O'Neill, F. H.

2016-01-01

This study evaluated membrane stabilization and detoxification potential of ethyl acetate fraction of Zea mays L., Stigma maydis in acetaminophen-induced oxidative onslaughts in the kidneys of Wistar rats. Nephrotoxic rats were orally pre- and posttreated with the fraction and vitamin C for 14 days. Kidney function, antioxidative and histological analyses were thereafter evaluated. The acetaminophen-mediated significant elevations in the serum concentrations of creatinine, urea, uric acid, sodium, potassium, and tissue levels of oxidized glutathione, protein-oxidized products, lipid peroxidized products, and fragmented DNA were dose-dependently assuaged in the fraction-treated animals. The fraction also markedly improved creatinine clearance rate, glutathione, and calcium concentrations as well as activities of superoxide dismutase, catalase, glutathione reductase, and glutathione peroxidase in the nephrotoxic rats. These improvements may be attributed to the antioxidative and membrane stabilization activities of the fraction. The observed effects compared favorably with that of vitamin C and are informative of the fraction's ability to prevent progression of renal pathological conditions and preserve kidney functions as evidently supported by the histological analysis. Although the effects were prominently exhibited in the fraction-pretreated groups, the overall data from the present findings suggest that the fraction could prevent or extenuate acetaminophen-mediated oxidative renal damage via fortification of antioxidant defense mechanisms. PMID:27579048

Detection of fungal infectous agent of wheat grains in store-pits of Markazi province, Iran.

PubMed

Saberi-Riseh, R; Javan-Nikkhah, M; Heidarian, R; Hosseini, S; Soleimani, P

2004-01-01

Wheat is an economic and important crop that provides approximately 20% of food calorie in the world. It is first crop in Iran and cultivated in the most areas of this country. Store-pit fungi make undesirable changes in quality and appearance of wheat grains. Even, some fungi produce different mycotoxins which are toxic to human and livestock's that use wheat grains as source of food. In this study, several samples were randomly collected from each of five store-pits located in different areas of Markazi Province including: Arak, Mahallat, Khomein, Saveh and Sarband. Grains were treated on PDA, and blotter, agar and washing test also used for isolating and detection of fungi. At least 100 grains per each sample were randomly used for each test and treatment. The fungi that determined in this study were Cochliobolus australiensis, Cladosporium herbarum, Epicoccum sp., Tilletia leavis, Aspergillus flavus, A. niger, A. fumigatus, Alternaria alternata, Alternaria sp., Penicillium italicum, P. digitatum, Fusarium sp., Rhizopus sp., Ustilago tritici, Scytalidium sp. Among these fungi the most isolates were belonged to Cladosporium, Alternaria, Rhizopus and Fusarium. Cladosporium herbarum was the most common in different sampling areas. Tilletia laevis and Ustilago tritici were just recovered in washing test. This study revealed that different fungi are associated with wheat grains in store-pits in Markazi Province. Some of them like Aspergillus flavus normally produce aflatoxin, a very toxic and carcinogenic mycotoxin that is harmful for human.

A Technical and Practical Study of Composting as a Solid Waste Management Alternative for the Air Force

DTIC Science & Technology

1992-09-01

eye) until the course of the process nears its end. When they do become apparent, they appear as a blue-gray to light green powdery to somewhat...clippings 3-6 12-15 Nonlegume vegetable wastes 2.5-4 11-12 Mixed grasses 214 19 Paper nil --- Potato tops 1.5 25 Straw, wheat 0.3-0.5 128-150 Straw, oats...Certain Fungal Plant Pathogens Organisms Disease Temperature (°C) Ustilago avenae Loose oat smut 45-53 0C U. tritici Loose smut of wheat 45-480 C U. zeae

Efficacy of Newer Molecules, Bioagents and Botanicals against Maydis Leaf Blight and Banded Leaf and Sheath Blight of Maize

PubMed Central

Malik, Vinod Kumar; Singh, Manjeet; Hooda, Karambir Singh; Yadav, Naresh Kumar; Chauhan, Prashant Kumar

2018-01-01

Maize (Zea mays L.; 2N=20) is major staple food crop grown worldwide adapted to several biotic and abiotic stresses. Maydis leaf blight (MLB) and banded leaf and sheath blight (BLSB) are serious foliar fungal diseases may cause up to 40% and 100% grain yield loss, respectively. The present studies were undertaken to work out the efficacy of chemicals, botanicals and bioagents for the management of MLB and BLSB under field condition for two seasons Kharif 2014 and 2015. Five molecules (propiconazole 25 EC, hexaconazole 25 EC, carbendazim 50 WP, mancozeb 75 WP and carbedazim 12 WP + mancozeb 63 WP), two bioagents i.e. Trichoderma harzianum and T. viridae and three botanicals namely azadirachtin, sarpagandha and bel pathar were tested for their efficacy against MLB. Eight newer fungicides viz., difenconazole 250 SC, hexaconazole 5 EC, carbendazim 50WP, validamycin 3 L, tebuconazole 250 EC, trifloxystrobin 50 WG + tebuconazole 50 WG, azoxystrobin 250 EC and pencycuron 250 SC were evaluated against BLSB. Analysis revealed significant effects of propiconazole at 0.1%, carbendazim 12 WP + mancozeb 63 WP at 0.125% and sarpagandha leaves at 10% against MLB pathogen, whereas validamycin at 0.1% and trifloxystrobin 25 WG + tebuconazole 50 WG at 0.05% were found effective against BLSB. The slow rate of disease control virtually by the bioagents might have not shown instant effect on plant response to the yield enhancing components. The identified sources of management can be used further in strengthening the plant protection in maize against MLB and BLSB. PMID:29628818

Efficacy of Newer Molecules, Bioagents and Botanicals against Maydis Leaf Blight and Banded Leaf and Sheath Blight of Maize.

PubMed

Malik, Vinod Kumar; Singh, Manjeet; Hooda, Karambir Singh; Yadav, Naresh Kumar; Chauhan, Prashant Kumar

2018-04-01

Maize ( Zea mays L.; 2N=20) is major staple food crop grown worldwide adapted to several biotic and abiotic stresses. Maydis leaf blight (MLB) and banded leaf and sheath blight (BLSB) are serious foliar fungal diseases may cause up to 40% and 100% grain yield loss, respectively. The present studies were undertaken to work out the efficacy of chemicals, botanicals and bioagents for the management of MLB and BLSB under field condition for two seasons Kharif 2014 and 2015. Five molecules (propiconazole 25 EC, hexaconazole 25 EC, carbendazim 50 WP, mancozeb 75 WP and carbedazim 12 WP + mancozeb 63 WP), two bioagents i.e. Trichoderma harzianum and T. viridae and three botanicals namely azadirachtin, sarpagandha and bel pathar were tested for their efficacy against MLB. Eight newer fungicides viz., difenconazole 250 SC, hexaconazole 5 EC, carbendazim 50WP, validamycin 3 L, tebuconazole 250 EC, trifloxystrobin 50 WG + tebuconazole 50 WG, azoxystrobin 250 EC and pencycuron 250 SC were evaluated against BLSB. Analysis revealed significant effects of propiconazole at 0.1%, carbendazim 12 WP + mancozeb 63 WP at 0.125% and sarpagandha leaves at 10% against MLB pathogen, whereas validamycin at 0.1% and trifloxystrobin 25 WG + tebuconazole 50 WG at 0.05% were found effective against BLSB. The slow rate of disease control virtually by the bioagents might have not shown instant effect on plant response to the yield enhancing components. The identified sources of management can be used further in strengthening the plant protection in maize against MLB and BLSB.

Genetics of Ustilago violacea. XXXII. Genetic evidence for transposable elements.

PubMed

Garber, E D; Ruddat, M

1994-12-01

Crosses between Ustilago violacea mutant strains with different color phenotypes that were derived from the 1.A1 and 2.A2 laboratory strains yielded, as expected, bisectored teliospore colonies with the parental colors as well as the a-1 and the a-2 mating-types. Generally, wild teliospore collections usually produced sporidia of both mating-types, providing two-mating-type (TMT) strains. Occasionally, however, sporidia with only one mating-type allele, a-1 or a-2, were obtained from teliospores, providing one-mating-type (OMT) strains. Crosses between OMT and laboratory strains with different color phenotypes gave (1) bisectored teliospore colonies with the parental colors or colonies with a parental color and a nonparental color and (2) nonsectored colonies with the nonparental color or with the parental color. The frequencies for the occurrence of non-parental color ranged from 41% to 93%, depending on the strain. The yield of teliospore colonies was usually reduced for these crosses. In many of these teliospore colonies, morphologically-altered sporidia (MAS phenotype) were observed. The morphology and the size of the sporidia with the MAS phenotype differed from those of teliospore colonies of the crosses between the laboratory strains. In addition, these sporidia did not form conjugants. A cross involving the TMT strains C449 yielded the MAS phenotype as well as a high incidence of tetrad colonies with a nonparental color. The high degree of instability of the parental color phenotypes, and the high frequency of the appearance of nonparental color phenotypes as well as the appearance of the MAS phenotype, are in accord with the presence of active and inactive transposable elements in the OMT strains, TMT strains, and laboratory strains.

Estimating the abundance of airborne pollen and fungal spores at variable elevations using an aircraft: how high can they fly?

PubMed

Damialis, Athanasios; Kaimakamis, Evangelos; Konoglou, Maria; Akritidis, Ioannis; Traidl-Hoffmann, Claudia; Gioulekas, Dimitrios

2017-03-16

Airborne pollen and fungal spores are monitored mainly in highly populated, urban environments, for allergy prevention purposes. However, their sources can frequently be located outside cities' fringes with more vegetation. So as to shed light to this paradox, we investigated the diversity and abundance of airborne pollen and fungal spores at various environmental regimes. We monitored pollen and spores using an aircraft and a car, at elevations from sea level to 2,000 m above ground, in the region of Thesssaloniki, Greece. We found a total of 24 pollen types and more than 15 spore types. Pollen and spores were detected throughout the elevational transect. Lower elevations exhibited higher pollen concentrations in only half of plant taxa and higher fungal spore concentrations in only Ustilago. Pinaceae and Quercus pollen were the most abundant recorded by airplane (>54% of the total). Poaceae pollen were the most abundant via car measurements (>77% of the total). Cladosporium and Alternaria spores were the most abundant in all cases (aircraft: >69% and >17%, car: >45% and >27%, respectively). We conclude that pollen and fungal spores can be diverse and abundant even outside the main source area, evidently because of long-distance transport incidents.

Estimating the abundance of airborne pollen and fungal spores at variable elevations using an aircraft: how high can they fly?

NASA Astrophysics Data System (ADS)

Damialis, Athanasios; Kaimakamis, Evangelos; Konoglou, Maria; Akritidis, Ioannis; Traidl-Hoffmann, Claudia; Gioulekas, Dimitrios

2017-03-01

Airborne pollen and fungal spores are monitored mainly in highly populated, urban environments, for allergy prevention purposes. However, their sources can frequently be located outside cities’ fringes with more vegetation. So as to shed light to this paradox, we investigated the diversity and abundance of airborne pollen and fungal spores at various environmental regimes. We monitored pollen and spores using an aircraft and a car, at elevations from sea level to 2,000 m above ground, in the region of Thesssaloniki, Greece. We found a total of 24 pollen types and more than 15 spore types. Pollen and spores were detected throughout the elevational transect. Lower elevations exhibited higher pollen concentrations in only half of plant taxa and higher fungal spore concentrations in only Ustilago. Pinaceae and Quercus pollen were the most abundant recorded by airplane (>54% of the total). Poaceae pollen were the most abundant via car measurements (>77% of the total). Cladosporium and Alternaria spores were the most abundant in all cases (aircraft: >69% and >17%, car: >45% and >27%, respectively). We conclude that pollen and fungal spores can be diverse and abundant even outside the main source area, evidently because of long-distance transport incidents.

Estimating the abundance of airborne pollen and fungal spores at variable elevations using an aircraft: how high can they fly?

PubMed Central

Damialis, Athanasios; Kaimakamis, Evangelos; Konoglou, Maria; Akritidis, Ioannis; Traidl-Hoffmann, Claudia; Gioulekas, Dimitrios

2017-01-01

Airborne pollen and fungal spores are monitored mainly in highly populated, urban environments, for allergy prevention purposes. However, their sources can frequently be located outside cities’ fringes with more vegetation. So as to shed light to this paradox, we investigated the diversity and abundance of airborne pollen and fungal spores at various environmental regimes. We monitored pollen and spores using an aircraft and a car, at elevations from sea level to 2,000 m above ground, in the region of Thesssaloniki, Greece. We found a total of 24 pollen types and more than 15 spore types. Pollen and spores were detected throughout the elevational transect. Lower elevations exhibited higher pollen concentrations in only half of plant taxa and higher fungal spore concentrations in only Ustilago. Pinaceae and Quercus pollen were the most abundant recorded by airplane (>54% of the total). Poaceae pollen were the most abundant via car measurements (>77% of the total). Cladosporium and Alternaria spores were the most abundant in all cases (aircraft: >69% and >17%, car: >45% and >27%, respectively). We conclude that pollen and fungal spores can be diverse and abundant even outside the main source area, evidently because of long-distance transport incidents. PMID:28300143

Fungicide selective for basidiomycetes.

PubMed

Edgington, L V; Walton, G S; Miller, P M

1966-07-15

Concentrations of 2,3-dihydro-5-carboxanilido-6-methyl-1,4-oxathiin lower than 8 parts per million prevented mycelial growth of a number of Basidiomycetes. By contrast, mycelial growth of various other fungi-Phycomycetes, Ascomycetes, and Deuteromycetes-was 50 percent inhibited only by concentrations of 32 ppm or higher. Two exceptions to this pattern of selective fungitoxicity were found:an isolate of Rhizoctonia solani was not as sensitive as other Basidiomycetes, and the deuteromycete Verticillium alboatrum was inhibited by lower concentrations than affected other fungi in this group. Spore germination of two Basidiomycetes, Uromyces phaseoli and Ustilago nuda, was inhibited 95 percent or more at 10 ppm.

Fine mapping and identification of a candidate gene for the barley Un8 true loose smut resistance gene.

PubMed

Zang, Wen; Eckstein, Peter E; Colin, Mark; Voth, Doug; Himmelbach, Axel; Beier, Sebastian; Stein, Nils; Scoles, Graham J; Beattie, Aaron D

2015-07-01

The candidate gene for the barley Un8 true loose smut resistance gene encodes a deduced protein containing two tandem protein kinase domains. In North America, durable resistance against all known isolates of barley true loose smut, caused by the basidiomycete pathogen Ustilago nuda (Jens.) Rostr. (U. nuda), is under the control of the Un8 resistance gene. Previous genetic studies mapped Un8 to the long arm of chromosome 5 (1HL). Here, a population of 4625 lines segregating for Un8 was used to delimit the Un8 gene to a 0.108 cM interval on chromosome arm 1HL, and assign it to fingerprinted contig 546 of the barley physical map. The minimal tilling path was identified for the Un8 locus using two flanking markers and consisted of two overlapping bacterial artificial chromosomes. One gene located close to a marker co-segregating with Un8 showed high sequence identity to a disease resistance gene containing two kinase domains. Sequence of the candidate gene from the parents of the segregating population, and in an additional 19 barley lines representing a broader spectrum of diversity, showed there was no intron in alleles present in either resistant or susceptible lines, and fifteen amino acid variations unique to the deduced protein sequence in resistant lines differentiated it from the deduced protein sequences in susceptible lines. Some of these variations were present within putative functional domains which may cause a loss of function in the deduced protein sequences within susceptible lines.

Kinetics of α-amylase and α-glucosidase inhibitory potential of Zea mays Linnaeus (Poaceae), Stigma maydis aqueous extract: An in vitro assessment.

PubMed

Sabiu, S; O'Neill, F H; Ashafa, A O T

2016-05-13

Corn silk (Zea mays L., Stigma maydis) is an important herb used traditionally in many parts of the world to treat array of diseases including diabetes mellitus. Inhibitors of α-amylase and α-glucosidase offer an effective strategy to modulate levels of post prandial hyperglycaemia via control of starch metabolism. This study evaluated α-amylase and α-glucosidase inhibitory potentials of corn silk aqueous extract. Active principles and antioxidant attributes of the extract were also analysed. The α-amylase inhibitory potential of the extract was investigated by reacting its different concentrations with α-amylase and starch solution, while α-glucosidase inhibition was determined by pre-incubating α-glucosidase with different concentrations of the extract followed by addition of p-nitrophenylglucopyranoside. The mode(s) of inhibition of the enzymes were determined using Lineweaver-Burke plot. In vitro analysis of the extract showed that it exhibited potent and moderate inhibitory potential against α-amylase and α-glucosidase, respectively. The inhibition was concentration-dependent with respective half-maximal inhibitory concentration (IC50) values of 5.89 and 0.93mg/mL. Phytochemical analyses revealed the presence of alkaloids, flavonoids, phenols, saponins, tannins and phytosterols as probable inhibitory constituents. Furthermore, the extract remarkably scavenges reactive oxygen species like DPPH and nitric oxide radicals, elicited good reducing power and a significant metal chelating attributes. Overall, the non-competitive and uncompetitive mechanism of action of corn silk extract is due to its inhibitory effects on α-amylase and α-glucosidase, respectively. Consequently, this will reduce the rate of starch hydrolysis, enhance palliated glucose levels, and thus, lending credence to hypoglycaemic candidature of corn silk. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

[Screening of antifungi endophytic actinomyces strains from salvia przewalskii in Tibean Plateau].

PubMed

Liu, Song-Qing; Jiang, Hua-Ming; Guan, Tong-Wei; Qi, Shan-Shan; Gu, Yun-Fu; Zhao, Ke; Wang, Xu; Zhang, Xiao-Ping

2013-10-01

Twenty-four endophytic actinomycetes strains were isolated from the Salvia przewalskii in Tibetan Plateau of China by tablet coating method. Fusarium moniliforme, Helminthosporium turcicum and Bipolaris maydis were selected as indicator fungi to test the antimicrobial activities of these endophytic actinomycetes by tablet confrontation method. The results showed that 21 strains can produce antimicrobial substances which accounts for 85.7% of the total separates number. Four strains of endogenous actinomyces have more obvious antifungi activity. According to results of morphology and culture properties and 16S rDNA sequences of endophytic actinomyces, it is concluded that all of the isolates were streptomycetes trains.

A survey of pre-harvest ear rot diseases of maize and associated mycotoxins in south and central Zambia.

PubMed

Mukanga, Mweshi; Derera, John; Tongoona, Pangirayi; Laing, Mark D

2010-07-15

Maize ear rots reduce grain yield and quality with implication on food security and health. Some of the pathogenic fungi produce mycotoxins in maize grain posing a health risk to humans and livestock. Unfortunately, the levels of ear rot and mycotoxin infection in grain produced by subsistence farmers in sub-Saharan countries are not known. A survey was thus conducted to determine the prevalence of the ear rot problem and levels of mycotoxins in maize grain. A total of 114 farmsteads were randomly sampled from 11 districts in Lusaka and southern provinces in Zambia during 2006. Ten randomly picked cobs were examined per farmstead and the ear rot disease incidence and severity were estimated on site. This was followed by the standard seed health testing procedures for fungal isolation in the laboratory. Results indicated that the dominant ear rots were caused by Fusarium and Stenocarpella. Incidence of Fusarium verticillioides ranged from 2 to 21%, whereas that of Stenocarpella maydis reached 37% on ear rot diseased maize grain. In addition, 2-7% F. verticillioides, and 3-18% Aspergillus flavus, respectively, were recovered from seemingly healthy maize grain. The mean rank of fungal species, from highest to lowest, was F. verticillioides, S. maydis, A. flavus, Fusarium graminearum, Aspergillus niger, Penicillium spp., Botrydiplodia spp., and Cladosporium spp. The direct competitive ELISA-test indicated higher levels of fumonisins than aflatoxins in pre-harvest maize grain samples. The concentration of fumonisins from six districts, and aflatoxin from two districts, was 10-fold higher than 2 ppm and far higher than 2 ppb maximum daily intake recommended by the FAO/WHO. The study therefore suggested that subsistence farmers and consumers in this part of Zambia, and maybe also in similar environments in sub-Saharan Africa, might be exposed to dangerous levels of mycotoxins due to the high levels of ear rot infections in maize grain. 2010 Elsevier B.V. All rights reserved.

Selective Inhibition of K+, Na+, Cl−, and PO43− Uptake in Zea mays L. by Bipolaris (Helminthosporium) maydis Race T Pathotoxin

PubMed Central

Mertz, Stuart M.; Arntzen, Charles J.

1977-01-01

Pathotoxin preparations were obtained from either axenic culture filtrate of race T of Bipolaris maydis (Nisikado) Shoemaker (new culture media and toxin purification procedures are described) or extracts of maize leaves infected with the fungus. The toxins (10−6 to 10−8m) caused inhibition of [86Rb]K+ uptake in leaf discs and apical root segments of Zea mays L. cv W64A Texas (Tcms) and normal (N) cytoplasms. Significant inhibition was measurable as early as 5 min after adding toxin. In Tcms per cent inhibition was increased by increasing toxin concentration and time in toxin, by using solution at pH 5 rather than pH 7, by decreasing external KCl concentration over the range 50 to 0.1 mm (in the presence of 0.5 mm CaSO4), or by exposing leaf discs to light rather than dark during the uptake period in toxin. Root uptake of 22Na+ and 36Cl− was inhibited to a lesser extent than K+. Inhibition of 32PO43− uptake occurred after 40 min when cyclosis had ceased. When combined with data in the literature, our data indicate that the plasmalemma is the probable primary site of toxin action in N and Tcms maize. Comparison of the effects of toxin on K+ uptake in N and Tcms maize suggests the existence of more than one mode of toxin action: a weak disruptive effect in N and Tcms, and in addition, specific membrane sites in Tcms involved in monovalent ion uptake. Six genotypes in N or Tcms cytoplasm which exhibited different degrees of disease susceptibility in the field showed a corresponding gradation of susceptibility to the toxin when a K+ uptake bioassay was used. This correlation is strong evidence that the sites of toxin action affecting K+ transport have characteristics closely related to cellular factors regulating susceptibility to fungal attack. PMID:16660094

Candida spencermartinsiae sp. nov., Candida taylorii sp. nov. and Pseudozyma abaconensis sp. nov., novel yeasts from mangrove and coral reef ecosystems.

PubMed

Statzell-Tallman, Adele; Scorzetti, Gloria; Fell, Jack W

2010-08-01

Three species of yeasts are taxonomically described for strains isolated from marine environments. Candida spencermartinsiae sp. nov. (type strain CBS 10894T =NRRL Y-48663T) and Candida taylorii sp. nov. (type strain CBS 8508T =NRRL Y-27213T) are anamorphic ascomycetous yeasts in a phylogenetic cluster of marine yeasts in the Debaryomyces/Lodderomyces clade of the Saccharomycetales. The two species were isolated from multiple locations among coral reefs and mangrove habitats. Pseudozyma abaconensis sp. nov. (type strain CBS 8380T =NRRL Y-17380T) is an anamorphic basidiomycete that is related to the smut fungi of the genus Ustilago in the Ustilaginales. P. abaconensis was collected from waters adjacent to a coral reef.

Simple sequence repeat markers useful for sorghum downy mildew (Peronosclerospora sorghi) and related species

PubMed Central

Perumal, Ramasamy; Nimmakayala, Padmavathi; Erattaimuthu, Saradha R; No, Eun-Gyu; Reddy, Umesh K; Prom, Louis K; Odvody, Gary N; Luster, Douglas G; Magill, Clint W

2008-01-01

Background A recent outbreak of sorghum downy mildew in Texas has led to the discovery of both metalaxyl resistance and a new pathotype in the causal organism, Peronosclerospora sorghi. These observations and the difficulty in resolving among phylogenetically related downy mildew pathogens dramatically point out the need for simply scored markers in order to differentiate among isolates and species, and to study the population structure within these obligate oomycetes. Here we present the initial results from the use of a biotin capture method to discover, clone and develop PCR primers that permit the use of simple sequence repeats (microsatellites) to detect differences at the DNA level. Results Among the 55 primers pairs designed from clones from pathotype 3 of P. sorghi, 36 flanked microsatellite loci containing simple repeats, including 28 (55%) with dinucleotide repeats and 6 (11%) with trinucleotide repeats. A total of 22 microsatellites with CA/AC or GT/TG repeats were the most abundant (40%) and GA/AG or CT/TC types contribute 15% in our collection. When used to amplify DNA from 19 isolates from P. sorghi, as well as from 5 related species that cause downy mildew on other hosts, the number of different bands detected for each SSR primer pair using a LI-COR- DNA Analyzer ranged from two to eight. Successful cross-amplification for 12 primer pairs studied in detail using DNA from downy mildews that attack maize (P. maydis & P. philippinensis), sugar cane (P. sacchari), pearl millet (Sclerospora graminicola) and rose (Peronospora sparsa) indicate that the flanking regions are conserved in all these species. A total of 15 SSR amplicons unique to P. philippinensis (one of the potential threats to US maize production) were detected, and these have potential for development of diagnostic tests. A total of 260 alleles were obtained using 54 microsatellites primer combinations, with an average of 4.8 polymorphic markers per SSR across 34 Peronosclerospora, Peronospora and Sclerospora spp isolates studied. Cluster analysis by UPGMA as well as principal coordinate analysis (PCA) grouped the 34 isolates into three distinct groups (all 19 isolates of Peronosclerospora sorghi in cluster I, five isolates of P. maydis and three isolates of P. sacchari in cluster II and five isolates of Sclerospora graminicola in cluster III). Conclusion To our knowledge, this is the first attempt to extensively develop SSR markers from Peronosclerospora genomic DNA. The newly developed SSR markers can be readily used to distinguish isolates within several species of the oomycetes that cause downy mildew diseases. Also, microsatellite fragments likely include retrotransposon regions of DNA and these sequences can serve as useful genetic markers for strain identification, due to their degree of variability and their widespread occurrence among sorghum, maize, sugarcane, pearl millet and rose downy mildew isolates. PMID:19040756

High-density genetic mapping of a major QTL for resistance to multiple races of loose smut in a tetraploid wheat cross

PubMed Central

Kumar, Sachin; Knox, Ron E.; Singh, Asheesh K.; DePauw, Ron M.; Campbell, Heather L.; Isidro-Sanchez, Julio; Clarke, Fran R.; Pozniak, Curtis J.; N’Daye, Amidou; Meyer, Brad; Sharpe, Andrew; Ruan, Yuefeng; Cuthbert, Richard D.; Somers, Daryl; Fedak, George

2018-01-01

Loose smut, caused by Ustilago tritici (Pers.) Rostr., is a systemic disease of tetraploid durum wheat (Triticum turgidum L.). Loose smut can be economically controlled by growing resistant varieties, making it important to find and deploy new sources of resistance. Blackbird, a variety of T. turgidum L. subsp. carthlicum (Nevski) A. Love & D. Love, carries a high level of resistance to loose smut. Blackbird was crossed with the loose smut susceptible durum cultivar Strongfield to produce a doubled haploid (DH) mapping population. The parents and progenies were inoculated with U. tritici races T26, T32 and T33 individually and as a mixture at Swift Current, Canada in 2011 and 2012 and loose smut incidence (LSI) was assessed. Genotyping of the DH population and parents using an Infinium iSelect 90K single nucleotide polymorphism (SNP) array identified 12,952 polymorphic SNPs. The SNPs and 426 SSRs (previously genotyped in the same population) were mapped to 16 linkage groups spanning 3008.4 cM at an average inter-marker space of 0.2 cM in a high-density genetic map. Composite interval mapping analysis revealed three significant quantitative trait loci (QTL) for loose smut resistance on chromosomes 3A, 6B and 7A. The loose smut resistance QTL on 6B (QUt.spa-6B.2) and 7A (QUt.spa-7A.2) were derived from Blackbird. Strongfield contributed the minor QTL on 3A (QUt.spa-3A.2). The resistance on 6B was a stable major QTL effective against all individual races and the mixture of the three races; it explained up to 74% of the phenotypic variation. This study is the first attempt in durum wheat to identify and map loose smut resistance QTL using a high-density genetic map. The QTL QUt.spa-6B.2 would be an effective source for breeding resistance to multiple races of the loose smut pathogen because it provides near-complete broad resistance to the predominant virulence on the Canadian prairies. PMID:29485999

25S ribosomal RNA homologies of basidiomycetous yeasts: taxonomic and phylogenetic implications

NASA Technical Reports Server (NTRS)

Baharaeen, S.; Vishniac, H. S.

1984-01-01

Genera, families, and possibly orders of basidiomycetous yeasts can be defined by 25S rRNA homology and correlated phenotypic characters. The teleomorphic genera Filobasidium, Leucosporidium, and Rhodosporidium have greater than 96 relative binding percent (rb%) intrageneric 25S rRNA homology and significant intergeneric separation from each other and from Filobasidiella. The anamorphic genus Cryptococcus can be defined by morphology (monopolar budding), colony color, and greater than 75 rb% intrageneric homology; Vanrija is heterogeneous. Agaricostilbum (Phragmobasidiomycetes, Auriculariales), Hansenula (Ascomycotera, Endomycota), Tremella (Phragmobasidiomycetes, Tremellales), and Ustilago (Ustomycota, Ustilaginales) appear equally unrelated to the Cryptococcus, Filobasidiella, and Rhodosporidium spp. used as probes. The Filobasidiaceae and Sporidiaceae, Filobasidiales and Sporidiales, form coherent homology groups which appear to have undergone convergent 25S rRNA evolution, since their relatedness is much greater than that indicated by 5S rRNA homology. Ribosomal RNA homologies do not appear to measure evolutionary distance.

The role of effectors of biotrophic and hemibiotrophic fungi in infection.

PubMed

Koeck, Markus; Hardham, Adrienne R; Dodds, Peter N

2011-12-01

Biotrophic and hemibiotrophic fungi are successful groups of plant pathogens that require living plant tissue to survive and complete their life cycle. Members of these groups include the rust fungi and powdery mildews and species in the Ustilago, Cladosporium and Magnaporthe genera. Collectively, they represent some of the most destructive plant parasites, causing huge economic losses and threatening global food security. During plant infection, pathogens synthesize and secrete effector proteins, some of which are translocated into the plant cytosol where they can alter the host's response to the invading pathogen. In a successful infection, pathogen effectors facilitate suppression of the plant's immune system and orchestrate the reprogramming of the infected tissue so that it becomes a source of nutrients that are required by the pathogen to support its growth and development. This review summarizes our current understanding of the function of fungal effectors in infection. © 2011 Blackwell Publishing Ltd.

Identification of QTLs conferring resistance to downy mildews of maize in Asia.

PubMed

George, M L C; Prasanna, B M; Rathore, R S; Setty, T A S; Kasim, F; Azrai, M; Vasal, S; Balla, O; Hautea, D; Canama, A; Regalado, E; Vargas, M; Khairallah, M; Jeffers, D; Hoisington, D

2003-08-01

Downy mildew is one of the most destructive diseases of maize in subtropical and tropical regions in Asia. As a prerequisite for improving downy mildew resistance in maize, we analyzed quantitative trait loci (QTLs) involved in resistance to the important downy mildew pathogens--Peronosclerospora sorghi (sorghum downy mildew) and P. heteropogoni (Rajasthan downy mildew) in India, P. maydis (Java downy mildew) in Indonesia, P. zeae in Thailand and P. philippinensis in the Philippines--using a recombinant inbred line population derived from a cross between Ki3 (downy mildew resistant) and CML139 (susceptible). Resistance was evaluated as percentage disease incidence in replicated field trials at five downy mildew 'hotspots' in the four countries. Heritability estimates of individual environments ranged from 0.58 to 0.75 with an across environment heritability of 0.50. Composite interval mapping was applied for QTL detection using a previously constructed restriction fragment length polymorphism linkage map. The investigation resulted in the identification of six genomic regions on chromosomes 1, 2, 6, 7 and 10 involved in the resistance to the downy mildews under study, explaining, in total, 26-57% of the phenotypic variance for disease response. Most QTL alleles conferring resistance to the downy mildews were from Ki3. All QTLs showed significant QTL x environment interactions, suggesting that the expression of the QTL may be environment-dependent. A strong QTL on chromosome 6 was stable across environments, significantly affecting disease resistance at the five locations in four Asian countries. Simple-sequence repeat markers tightly linked to this QTL were identified for potential use in marker-assisted selection.

Fungal contamination and selected mycotoxins in pre- and post-harvest maize in Honduras.

PubMed

Julian, A M; Wareing, P W; Phillips, S I; Medlock, V F; MacDonald, M V; del Río, L E

1995-01-01

Sixty nine samples of maize were collected from pre-harvest standing crops and on-farm storage facilities from 52 smallholder farms located within 4 regions of Honduras during October 1992 and November 1993. Samples were visually assessed for insect damage and fungal spoilage, and the mycoflora quantified on artificial media. The major components of the ear rot complex were: Fusarium moniliforme, F. moniliforme var. subglutinans, Penicillium species, Stenocarpella maydis, S. macrospora and Acremonium spp. Representative samples were also assayed for mycotoxin content. Fumonisin B1 was detected in all 24 samples tested at levels of between 68-6,555 (micrograms/kg), and aflatoxin was detected in 2 samples heavily contaminated with Aspergillus flavus. Moniliformin and tenuazonic acid were not detected in the samples tested. The implications of these findings for human and livestock health risk are discussed, together with possible strategies for controlling these pathogens.

Spatial expression dynamics of Men-9 delineate the third floral whorl in male and female flowers of dioecious Silene latifolia.

PubMed

Robertson, S E; Li, Y; Scutt, C P; Willis, M E; Gilmartin, P M

1997-07-01

Sex determination in Silene latifolia is controlled by heteromorphic sex chromosomes. Female flowers have five fused carpels and ten arrested stamen primordia. The male-determining Y chromosome overrides female development to suppress carpel formation and promote stamen development. The isolation and characterization of two S. latifolia. Male enhanced cDNAs, Men-9a and Men-9b, which probably represent different alleles of a novel gene are reported here. Men-9a and Men-9b share 91.8% coding sequence nucleotide identity, yet only 85.4% amino acid identity. The Men-9 cDNAs are related to the previously reported MROS3 cDNA from S. latifolia. However, MROS3 is not present in the S. latifolia population used in these studies and the expression dynamics of Men-9a and Men-9b contrast dramatically with those reported for MROS3. Men-9 cDNAs are expressed primarily in anthers of young male flowers, with highest expression in 1-2 mm buds. Men-9 expression is also observed at a low level in female flowers. In situ hybridization analysis reveals two phases of Men-9 expression. The first phase is during a common stage of early stamen development in male and female flowers prior to stamen arrest in female flowers. The second phase of Men-9 expression is maximal in the epidermis and endothecium of Y chromosome- and Ustilago violacea-induced stamens; expression in male and female flowers extends to the epidermis of the staminal nectaries with strict boundaries at the second and fourth whorls, Men-9 gene expression therefore delineates the boundaries of the third floral whorl in S. latifolia flowers.

A host plant genome ( Zizania latifolia ) after a century-long endophyte infection

DOE PAGES

Guo, Longbiao; Qiu, Jie; Han, Zujing; ...

2015-06-13

In spite of the importance of host–microbe interactions in natural ecosystems, agriculture and medicine, the impact of long-term (especially decades or longer) microbial colonization on the dynamics of host genomes is not well understood. Moreover, the vegetable crop ‘Jiaobai’ with enlarged edible stems was domesticated from wild Zizania latifolia (Oryzeae) approximately 2000 years ago as a result of persistent infection by a fungal endophyte, Ustilago esculenta. Asexual propagation via infected rhizomes is the only means of Jiaobai production, and the Z. latifolia–endophyte complex has been maintained continuously for two centuries. Here, genomic analysis revealed that cultivated Z. latifolia has amore » significantly smaller repertoire of immune receptors compared with wild Z. latifolia. There are widespread gene losses/mutations and expression changes in the plant–pathogen interaction pathway in Jiaobai. Finally, these results show that continuous long-standing endophyte association can have a major effect on the evolution of the structural and transcriptomic components of the host genome.« less

In vivo insertion pool sequencing identifies virulence factors in a complex fungal–host interaction

PubMed Central

Uhse, Simon; Pflug, Florian G.; Stirnberg, Alexandra; Ehrlinger, Klaus; von Haeseler, Arndt

2018-01-01

Large-scale insertional mutagenesis screens can be powerful genome-wide tools if they are streamlined with efficient downstream analysis, which is a serious bottleneck in complex biological systems. A major impediment to the success of next-generation sequencing (NGS)-based screens for virulence factors is that the genetic material of pathogens is often underrepresented within the eukaryotic host, making detection extremely challenging. We therefore established insertion Pool-Sequencing (iPool-Seq) on maize infected with the biotrophic fungus U. maydis. iPool-Seq features tagmentation, unique molecular barcodes, and affinity purification of pathogen insertion mutant DNA from in vivo-infected tissues. In a proof of concept using iPool-Seq, we identified 28 virulence factors, including 23 that were previously uncharacterized, from an initial pool of 195 candidate effector mutants. Because of its sensitivity and quantitative nature, iPool-Seq can be applied to any insertional mutagenesis library and is especially suitable for genetically complex setups like pooled infections of eukaryotic hosts. PMID:29684023

Molecular variation of Sporisorium scitamineum in Mainland China revealed by internal transcribed spacers.

PubMed

Zhang, Y Y; Huang, N; Xiao, X H; Huang, L; Liu, F; Su, W H; Que, Y X

2015-07-14

Sugarcane smut caused by the fungus Sporisorium scitamineum is a worldwide disease and also one of the most prevalent diseases in sugarcane production in mainland China. To study molecular variation in S. scitamineum, 23 S. scitamineum isolates from the 6 primary sugar-cane production areas in mainland, China (Guangxi, Yunnan, Guangdong, Hainan, Fujian, and Jiangxi Provinces), were assessed using internal transcribed spacer (ITS) methods. The results of ITS sequence analysis showed that the organisms can be defined at the genus level, including Ustilago and Sporisorium, and can also differentiate between closely related species. This method was not suitable for phylogenetic relationship analysis of different S. scitamineum isolates and could not provide support regarding their race ascription at the molecular level. The results of the present study will be useful for studies examining the molecular diversity of S. scitamineum and for establishing a genetic foundation for their pathogenicity differentiation and new race detection. In addition, our results can provide useful information for the pathogen selection principle in sugarcane smut resistance breeding and variety distribution.

Fungal Planet description sheets: 214-280.

PubMed

Crous, P W; Shivas, R G; Quaedvlieg, W; van der Bank, M; Zhang, Y; Summerell, B A; Guarro, J; Wingfield, M J; Wood, A R; Alfenas, A C; Braun, U; Cano-Lira, J F; García, D; Marin-Felix, Y; Alvarado, P; Andrade, J P; Armengol, J; Assefa, A; den Breeÿen, A; Camele, I; Cheewangkoon, R; De Souza, J T; Duong, T A; Esteve-Raventós, F; Fournier, J; Frisullo, S; García-Jiménez, J; Gardiennet, A; Gené, J; Hernández-Restrepo, M; Hirooka, Y; Hospenthal, D R; King, A; Lechat, C; Lombard, L; Mang, S M; Marbach, P A S; Marincowitz, S; Marin-Felix, Y; Montaño-Mata, N J; Moreno, G; Perez, C A; Pérez Sierra, A M; Robertson, J L; Roux, J; Rubio, E; Schumacher, R K; Stchigel, A M; Sutton, D A; Tan, Y P; Thompson, E H; van der Linde, E; Walker, A K; Walker, D M; Wickes, B L; Wong, P T W; Groenewald, J Z

2014-06-01

Novel species of microfungi described in the present study include the following from South Africa: Cercosporella dolichandrae from Dolichandra unguiscati, Seiridium podocarpi from Podocarpus latifolius, Pseudocercospora parapseudarthriae from Pseudarthria hookeri, Neodevriesia coryneliae from Corynelia uberata on leaves of Afrocarpus falcatus, Ramichloridium eucleae from Euclea undulata and Stachybotrys aloeticola from Aloe sp. (South Africa), as novel member of the Stachybotriaceae fam. nov. Several species were also described from Zambia, and these include Chaetomella zambiensis on unknown Fabaceae, Schizoparme pseudogranati from Terminalia stuhlmannii, Diaporthe isoberliniae from Isoberlinia angolensis, Peyronellaea combreti from Combretum mossambiciensis, Zasmidium rothmanniae and Phaeococcomyces rothmanniae from Rothmannia engleriana, Diaporthe vangueriae from Vangueria infausta and Diaporthe parapterocarpi from Pterocarpus brenanii. Novel species from the Netherlands include: Stagonospora trichophoricola, Keissleriella trichophoricola and Dinemasporium trichophoricola from Trichophorum cespitosum, Phaeosphaeria poae, Keissleriella poagena, Phaeosphaeria poagena, Parastagonospora poagena and Pyrenochaetopsis poae from Poa sp., Septoriella oudemansii from Phragmites australis and Dendryphion europaeum from Hedera helix (Germany) and Heracleum sphondylium (the Netherlands). Novel species from Australia include: Anungitea eucalyptorum from Eucalyptus leaf litter, Beltraniopsis neolitseae and Acrodontium neolitseae from Neolitsea australiensis, Beltraniella endiandrae from Endiandra introrsa, Phaeophleospora parsoniae from Parsonia straminea, Penicillifer martinii from Cynodon dactylon, Ochroconis macrozamiae from Macrozamia leaf litter, Triposporium cycadicola, Circinotrichum cycadis, Cladosporium cycadicola and Acrocalymma cycadis from Cycas spp. Furthermore, Vermiculariopsiella dichapetali is described from Dichapetalum rhodesicum (Botswana), Ophiognomonia acadiensis from Picea rubens (Canada), Setophoma vernoniae from Vernonia polyanthes and Penicillium restingae from soil (Brazil), Pseudolachnella guaviyunis from Myrcianthes pungens (Uruguay) and Pseudocercospora neriicola from Nerium oleander (Italy). Novelties from Spain include: Dendryphiella eucalyptorum from Eucalyptus globulus, Conioscypha minutispora from dead wood, Diplogelasinospora moalensis and Pseudoneurospora canariensis from soil and Inocybe lanatopurpurea from reforested woodland of Pinus spp. Novelties from France include: Kellermania triseptata from Agave angustifolia, Zetiasplozna acaciae from Acacia melanoxylon, Pyrenochaeta pinicola from Pinus sp. and Pseudonectria rusci from Ruscus aculeatus. New species from China include: Dematiocladium celtidicola from Celtis bungeana, Beltrania pseudorhombica, Chaetopsina beijingensis and Toxicocladosporium pini from Pinus spp. and Setophaeosphaeria badalingensis from Hemerocallis fulva. Novel genera of Ascomycetes include Alfaria from Cyperus esculentus (Spain), Rinaldiella from a contaminated human lesion (Georgia), Hyalocladosporiella from Tectona grandis (Brazil), Pseudoacremonium from Saccharum spontaneum and Melnikomyces from leaf litter (Vietnam), Annellosympodiella from Juniperus procera (Ethiopia), Neoceratosperma from Eucalyptus leaves (Thailand), Ramopenidiella from Cycas calcicola (Australia), Cephalotrichiella from air in the Netherlands, Neocamarosporium from Mesembryanthemum sp. and Acervuloseptoria from Ziziphus mucronata (South Africa) and Setophaeosphaeria from Hemerocallis fulva (China). Several novel combinations are also introduced, namely for Phaeosphaeria setosa as Setophaeosphaeria setosa, Phoma heteroderae as Peyronellaea heteroderae and Phyllosticta maydis as Peyronellaea maydis. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.

A novel and exploitable antifungal peptide from kale (Brassica alboglabra) seeds.

PubMed

Lin, Peng; Ng, Tzi Bun

2008-10-01

The aim of this study was to purify and characterize antifungal peptides from kale seeds in view of the paucity of information on antifungal peptides from the family Brassicaceae, and to compare its characteristics with those of published Brassica antifungal peptides. A 5907-Da antifungal peptide was isolated from kale seeds. The isolation procedure comprised affinity chromatography on Affi-gel blue gel, ion exchange chromatography on SP-Sepharose and Mono S, and gel filtration on Superdex Peptide. The peptide was adsorbed on the first three chromatographic media. It inhibited mycelial growth in a number of fungal species including Fusarium oxysporum, Helminthosporium maydis, Mycosphaerella arachidicola and Valsa mali, with an IC(50) of 4.3microM, 2.1microM, 2.4microM, and 0.15microM, respectively and exhibited pronounced thermostability and pH stability. It inhibited proliferation of hepatoma (HepG2) and breast cancer (MCF7) cells with an IC(50) of 2.7microM and 3.4microM, and the activity of HIV-1 reverse transcriptase with an IC(50) of 4.9microM. Its N-terminal sequence differed from those of antifungal proteins which have been reported to date.

First report of an anti-tumor, anti-fungal, anti-yeast and anti-bacterial hemolysin from Albizia lebbeck seeds.

PubMed

Lam, Sze Kwan; Ng, Tzi Bun

2011-05-15

A monomeric 5.5-kDa protein with hemolytic activity toward rabbit erythrocytes was isolated from seeds of Albizia lebbeck by using a protocol that involved ion-exchange chromatography on Q-Sepharose and SP-Sepharose, hydrophobic interaction chromatography on Phenyl-Sepharose, and gel filtration on Superdex 75. It was unadsorbed on both Q-Sepharose and SP-Sepharose, but adsorbed on Phenyl-Sepharose. Its hemolytic activity was fully preserved in the pH range 0-14 and in the temperature range 0-100 °C, and unaffected in the presence of a variety of metal ions and carbohydrates. The hemolysin reduced viability of murine splenocytes and inhibited proliferation of MCF-7 breast cancer cells and HepG2 hepatoma cells with an IC₅₀ of 0.21, 0.97, and 1.37 μM, respectively. It impeded mycelial growth in the fungi Rhizoctonia solani with an IC₅₀ of 39 μM but there was no effect on a variety of other filamentous fungi, including Fusarium oxysporum, Helminthosporium maydis, Valsa mali and Mycosphaerella arachidicola. Lebbeckalysin inhibited growth of Escherichia coli with an IC₅₀ of 0.52 μM. Copyright © 2010 Elsevier GmbH. All rights reserved.

Semiautomated confocal imaging of fungal pathogenesis on plants: Microscopic analysis of macroscopic specimens.

PubMed

Minker, Katharine R; Biedrzycki, Meredith L; Kolagunda, Abhishek; Rhein, Stephen; Perina, Fabiano J; Jacobs, Samuel S; Moore, Michael; Jamann, Tiffany M; Yang, Qin; Nelson, Rebecca; Balint-Kurti, Peter; Kambhamettu, Chandra; Wisser, Randall J; Caplan, Jeffrey L

2018-02-01

The study of phenotypic variation in plant pathogenesis provides fundamental information about the nature of disease resistance. Cellular mechanisms that alter pathogenesis can be elucidated with confocal microscopy; however, systematic phenotyping platforms-from sample processing to image analysis-to investigate this do not exist. We have developed a platform for 3D phenotyping of cellular features underlying variation in disease development by fluorescence-specific resolution of host and pathogen interactions across time (4D). A confocal microscopy phenotyping platform compatible with different maize-fungal pathosystems (fungi: Setosphaeria turcica, Cochliobolus heterostrophus, and Cercospora zeae-maydis) was developed. Protocols and techniques were standardized for sample fixation, optical clearing, species-specific combinatorial fluorescence staining, multisample imaging, and image processing for investigation at the macroscale. The sample preparation methods presented here overcome challenges to fluorescence imaging such as specimen thickness and topography as well as physiological characteristics of the samples such as tissue autofluorescence and presence of cuticle. The resulting imaging techniques provide interesting qualitative and quantitative information not possible with conventional light or electron 2D imaging. Microsc. Res. Tech., 81:141-152, 2018. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

[Tablets and tablet production - with special reference to Icelandic conditions].

PubMed

Skaftason, Jóhannes F; Jóhannesson, Thorkell

2013-04-01

Modern tablet compression was instituted in England in 1844 by William Brockedon (1787-1854). The first tablets made according to Brockedon´s procedures contained watersoluble salts and were most likely compressed without expedients. In USA a watershed occurred around 1887 when starch (amylum maydis) was introduced to disperse tablets in aqueous milieu in order to corroborate bioavailability of drugs in the almentary canal. About the same time great advances in tablet production were introduced by the British firm Burroughs Wellcome and Co. In Denmark on the other hand tablet production remained on low scale until after 1920. As Icelandic pharmacies and drug firms modelled themselves mostly upon Danish firms tablet production was first instituted in Iceland around 1930. The first tablet machines in Iceland were hand-driven. More efficent machines came after 1945. Around 1960 three sizeable tablet producers were in Iceland; now there is only one. Numbers of individual tablet species (generic and proprietary) on the market rose from less than 10 in 1913 to 500 in 1965, with wide variations in numbers in between. Tablets have not wiped out other medicinal forms for peroral use but most new peroral drugs have been marketed in the form of tablets during the last decades.

Antimicrobial activity of pyrrocidines from Acremonium zeae against endophytes and pathogens of maize.

PubMed

Wicklow, Donald T; Poling, Stephen M

2009-01-01

Acremonium zeae produces pyrrocidines A and B, which are polyketide-amino acid-derived antibiotics, and is recognized as a seedborne protective endophyte of maize which augments host defenses against microbial pathogens causing seedling blights and stalk rots. Pyrrocidine A displayed significant in vitro activity against Aspergillus flavus and Fusarium verticillioides in assays performed using conidia as inoculum, with pyrrocidine A being more active than B. In equivalent assays performed with conidia or hyphal cells as inoculum, pyrrocidine A revealed potent activity against major stalk and ear rot pathogens of maize, including F. graminearum, Nigrospora oryzae, Stenocarpella (Diplodia) maydis, and Rhizoctonia zeae. Pyrrocidine A displayed significant activity against seed-rotting saprophytes A. flavus and Eupenicillium ochrosalmoneum, as well as seed-infecting colonists of the phylloplane Alternaria alternata, Cladosporium cladosporioides, and Curvularia lunata, which produces a damaging leaf spot disease. Protective endophytes, including mycoparasites which grow asymptomatically within healthy maize tissues, show little sensitivity to pyrrocidines. Pyrrocidine A also exhibited potent activity against Clavibacter michiganense subsp. nebraskense, causal agent of Goss's bacterial wilt of maize, and Bacillus mojaviense and Pseudomonas fluorescens, maize endophytes applied as biocontrol agents, but were ineffective against the wilt-producing bacterium Pantoea stewartii.

Isolation of a Hemagglutinin with Potent Antiproliferative Activity and a Large Antifungal Defensin from Phaseolus vulgaris cv. Hokkaido Large Pinto Beans.

PubMed

Yin, Cuiming; Wong, Jack Ho; Ng, Tzi Bun

2015-06-10

Lectins (hemagglutinins) are defined as sugar-binding proteins or glycoproteins with various biological activities. A 60 kDa dimeric hemagglutinin with a blocked N-terminus was isolated in large yield (190 mg/60 g) from the common edible bean Phaseolus vulgaris cv. Hokkaido large pinto bean. Its hemagglutinating, antifungal, and antitumor activities as well as the effects of carbohydrate and metal ions on its hemagglutinating activity were examined. It inhibited the proliferation of nasopharyngeal carcinoma (CNE2), human breast cancer (MCF7), and hepatoma (HepG2) cells. The IC50 values toward HepG2, MCF7, and CNE2 cells after treatment for 48 h were 8.1, 6.07, and 7.49 μM, respectively, which were relatively low among lectins of different P. vulgaris cultivars. From the pinto beans, a 10888 Da antifungal peptide with similarity to plant defensins as revealed by mass spectroscopic analysis was also isolated with a yield of 3.2 mg of proteins from 60 g of beans. The large defensin was capable of inhibiting mycelial growth in Mycosphaerella arachidicola, Setosphaeria turcica, Bipolaris maydis, and Fusarium oxysporum but not in Valsa mali.

Diversity of Bacillus-like bacterial community in the sediments of the Bamenwan mangrove wetland in Hainan, China.

PubMed

Liu, Min; Cui, Ying; Chen, Yuqing; Lin, Xiangzhi; Huang, Huiqin; Bao, Shixiang

2017-03-01

Members of the genus Bacillus and related spore-forming genera are ubiquitous. However, Bacillus-like species isolated from marine sediments have attracted less interest than their terrestrial relatives. Here, we investigated the diversity of Bacillus-like bacterial communities in the sediments of the Bamenwan mangrove wetland in Hainan, China, using culture-dependent and culture-independent methods, and present the first report on this subject. We also discovered some potential novel species from the sediment samples. Four families, Bacillaceae (58%), Paenibacillaceae (22%), Alicyclobacillaceae (15%), and Planococcaceae (5%), and 9 genera, Bacillus (42%), Paenibacillus (16%), Halobacillus (13%), Alicyclobacillus (11%), Rummeliibacillus (5%), Cohnella (5%), Tumebacillus (4%), Pontibacillus (3%), and Aneurinibacillus (2%), were identified by pyrosequencing. In contrast, only 4 genera, Bacillus (57%), Paenibacillus (23%), Halobacillus (14%), and Virgibacillus (6%), were detected by the culture-dependent method. In the 16S rDNA sequencing analysis, the isolates HB12036 and HB12037 were closest to Bacillus okuhidensis Kh10-101 T and Paenibacillus xylanilyticus XIL14 T with similarities of 94.8% and 95.9%, respectively, indicating that these were novel species. Bacillus sp. HB12035 and HB12040 exhibited antimicrobial activity against Staphylococcus aureus ATCC 25923, and Bacillus sp. HB12033 exhibited antimicrobial activity against Ustilago scitaminea Syd.

Purification and characterization of a glucosamine-binding antifungal lectin from Phaseolus vulgaris cv. Chinese pinto beans with antiproliferative activity towards nasopharyngeal carcinoma cells.

PubMed

Ang, Andrew Si Wo; Cheung, Randy Chi Fai; Dan, Xiuli; Chan, Yau Sang; Pan, Wenliang; Ng, Tzi Bun

2014-01-01

A lectin has successfully been isolated from Phaseolus vulgaris cv. Chinese pinto bean using affinity chromatography, ion exchange chromatography, and gel filtration in succession, with a 15.4-fold purification. Investigation of its characteristics revealed that Chinese pinto bean lectin (CPBL) was a 58-kDa dimeric glucosamine-binding protein. Its Mg(2+)-dependent hemagglutinating activity was stable at pH 7-8 and at or below 60 °C. When the purified lectin was tested against six fungal species including Phyllosticta citriasiana, Magnaporthe grisea, Bipolans maydis, Valsa mali, Mycosphaerella arachidicola, and Setosphaeria turcica, only the mycelial growth of V. mali was reduced by 30.6 % by the lectin at 30 μM. The lectin did not exert any discernible antiproliferative effects on breast cancer MCF-7 cells, but was able to suppress proliferation of nasopharyngeal carcinoma HONE-1 cells, with an IC50 of 17.3 μM, as revealed by the MTT assay. Since few plant lectins demonstrate antifungal activity against V. mali, and not many others have inhibitory effects on HONE-1 cells, CPBL is a distinctive lectin which may be exploited for development into an agent against V. mali and HONE-1 cells.

Biological activity of sedaxane---a novel broad-spectrum fungicide for seed treatment.

PubMed

Zeun, Ronald; Scalliet, Gabriel; Oostendorp, Michael

2013-04-01

Sedaxane is a new broad-spectrum seed treatment fungicide developed by Syngenta Crop Protection for control of seed- and soil-borne diseases in a broad range of crops. Its physicochemical properties and activity spectrum have been optimised for use as a seed treatment providing both local and systemic protection of the seed and roots of target crops. Sedaxane inhibits respiration by binding to the succinate dehydrogenase complex in the fungal mitochondrium. Its activity spectrum covers seed-borne fungi such as Ustilago nuda, Tilletia caries, Monographella nivalis and Pyrenophora graminea, as well as the soil-borne fungi Rhizoctonia solani, R. cerealis and Typhula incarnata. Under greenhouse conditions, sedaxane showed high levels and consistent protection against U. nuda, P. graminea and Rhizoctonia spp. Under field conditions, efficacy against Rhizoctonia spp. resulted in increased yield compared with the untreated check. Efficacy against snow mould has been shown under very high disease pressure conditions. The combination of sedaxane plus fludioxonil against snow mould can provide resistance management for sustainable use. The broad spectrum and high level of activity in combination with excellent crop tolerance allow the use of sedaxane as a seed treatment in a wide variety of crops. It is a potential tool for precautionary resistance management when combined with other fungicides, especially against pathogens showing a potential for resistance development, such as M. nivalis. © 2012 Society of Chemical Industry.

Bioprospecting and evolving alternative xylose and arabinose pathway enzymes for use in Saccharomyces cerevisiae.

PubMed

Lee, Sun-Mi; Jellison, Taylor; Alper, Hal S

2016-03-01

Bioprospecting is an effective way to find novel enzymes from strains with desirable phenotypes. Such bioprospecting has enabled organisms such as Saccharomyces cerevisiae to utilize nonnative pentose sugars. Yet, the efficiency of this pentose catabolism (especially for the case of arabinose) remains suboptimal. Thus, further pathway optimization or identification of novel, optimal pathways is needed. Previously, we identified a novel set of xylan catabolic pathway enzymes from a superior pentose-utilizing strain of Ustilago bevomyces. These enzymes were used to successfully engineer a xylan-utilizing S. cerevisiae through a blended approach of bioprospecting and evolutionary engineering. Here, we expanded this approach to xylose and arabinose catabolic pathway engineering and demonstrated that bioprospected xylose and arabinose catabolic pathways from U. bevomyces offer alternative choices for enabling efficient pentose catabolism in S. cerevisiae. By introducing a novel set of xylose catabolic genes from U. bevomyces, growth rates were improved up to 85 % over a set of traditional Scheffersomyces stipitis pathway genes. In addition, we suggested an alternative arabinose catabolic pathway which, after directed evolution and pathway engineering, enabled S. cerevisiae to grow on arabinose as a sole carbon source in minimal medium with growth rates upwards of 0.05 h(-1). This pathway represents the most efficient growth of yeast on pure arabinose minimal medium. These pathways provide great starting points for further strain development and demonstrate the utility of bioprospecting from U. bevomyces.

The effects of meteorological factors on airborne fungal spore concentration in two areas differing in urbanisation level

NASA Astrophysics Data System (ADS)

Oliveira, M.; Ribeiro, H.; Delgado, J. L.; Abreu, I.

2009-01-01

Although fungal spores are an ever-present component of the atmosphere throughout the year, their concentration oscillates widely. This work aims to establish correlations between fungal spore concentrations in Porto and Amares and meteorological data. The seasonal distribution of fungal spores was studied continuously (2005-2007) using volumetric spore traps. To determine the effect of meteorological factors (temperature, relative humidity and rainfall) on spore concentration, the Spearman rank correlation test was used. In both locations, the most abundant fungal spores were Cladosporium, Agaricus, Agrocybe, Alternaria and Aspergillus/Penicillium, the highest concentrations being found during summer and autumn. In the present study, with the exception of Coprinus and Pleospora, spore concentrations were higher in the rural area than in the urban location. Among the selected spore types, spring-autumn spores ( Coprinus, Didymella, Leptosphaeria and Pleospora) exhibited negative correlations with temperature and positive correlations both with relative humidity and rainfall level. On the contrary, late spring-early summer (Smuts) and summer spores ( Alternaria, Cladosporium, Epicoccum, Ganoderma, Stemphylium and Ustilago) exhibited positive correlations with temperature and negative correlations both with relative humidity and rainfall level. Rust, a frequent spore type during summer, had a positive correlation with temperature. Aspergillus/Penicillium, showed no correlation with the meteorological factors analysed. This knowledge can be useful for agriculture, allowing more efficient and reliable application of pesticides, and for human health, by improving the diagnosis and treatment of respiratory allergic disease.

Tuber indicum shapes the microbial communities of ectomycorhizosphere soil and ectomycorrhizae of an indigenous tree (Pinus armandii)

PubMed Central

Li, Qiang; Zhao, Jian; Xiong, Chuan; Li, Xiaolin; Chen, Zuqin; Li, Ping; Huang, Wenli

2017-01-01

The aim of this study was to investigate the effect of an ectomycorrhizal fungus (Tuber indicum) on the diversity of microbial communities associated with an indigenous tree, Pinus armandii, and the microbial communities in the surrounding ectomycorhizosphere soil. High-throughput sequencing was used to analyze the richness of microbial communities in the roots or rhizosphere of treatments with or without ectomycorrhizae. The results indicated that the bacterial diversity of ectomycorhizosphere soil was significantly lower compared with the control soil. Presumably, the dominance of truffle mycelia in ectomycorhizosphere soil (80.91%) and ectomycorrhizae (97.64%) was the main factor that resulted in lower diversity and abundance of endophytic pathogenic fungi, including Fusarium, Monographella, Ustilago and Rhizopus and other competitive mycorrhizal fungi, such as Amanita, Lactarius and Boletus. Bacterial genera Reyranena, Rhizomicrobium, Nordella, Pseudomonas and fungal genera, Cuphophyllus, Leucangium, Histoplasma were significantly more abundant in ectomycorrhizosphere soil and ectomycorrhizae. Hierarchical cluster analysis of the similarities between rhizosphere and ectomycorrhizosphere soil based on the soil properties differed significantly, indicating the mycorrhizal synthesis may have a feedback effect on soil properties. Meanwhile, some soil properties were significantly correlated with bacterial and fungal diversity in the rhizosphere or root tips. Overall, this work illustrates the interactive network that exists among ectomycorrhizal fungi, soil properties and microbial communities associated with the host plant and furthers our understanding of the ecology and cultivation of T. indicum. PMID:28410376

Antifungal metabolites (monorden, monocillins I, II, III) from Colletotrichum graminicola, a systemic vascular pathogen of maize.

PubMed

Wicklow, Donald T; Jordan, Annalisa M; Gloer, James B

2009-12-01

Colletotrichum graminicola is a systemic vascular pathogen that causes anthracnose stalk rot and leaf blight of maize. In the course of an effort to explore the potential presence and roles of C. graminicola metabolites in maize, ethyl acetate extracts of solid substrate fermentations of several C. graminicola isolates from Michigan and Illinois were found to be active against Aspergillus flavus and Fusarium verticillioides, both mycotoxin-producing seed-infecting fungal pathogens. Chemical investigations of the extract of one such isolate (NRRL 47511) led to the isolation of known metabolites monorden (also known as radicicol) and monocillins I-III as major components. Monorden and monocillin I displayed in vitro activity against the stalk- and ear-rot pathogen Stenocarpella maydis while only the most abundant metabolite (monorden) showed activity against foliar pathogens Alternaria alternata, Bipolaris zeicola, and Curvularia lunata. Using LC-HRESITOFMS, monorden was detected in steam-sterilized maize stalks and stalk residues inoculated with C. graminicola but not in the necrotic stalk tissues of wound-inoculated plants grown in an environmental chamber. Monorden and monocillin I can bind and inhibit plant Hsp90, a chaperone of R-proteins. It is hypothesized that monorden and monocillins could support the C. graminicola disease cycle by disrupting maize plant defenses and by excluding other fungi from necrotic tissues and crop residues. This is the first report of natural products from C. graminicola, as well as the production of monorden and monocillins by a pathogen of cereals.

Preparation and mechanism analysis of an environment-friendly maize seed coating agent.

PubMed

Zeng, Defang; Fan, Zhao; Tian, Xu; Wang, Wenjin; Zhou, Mingchun; Li, Haochuan

2018-06-01

Traditional seed coating agents often contain toxic ingredients, which contaminate the environment and threaten human health. This paper expounds a method of preparing a novel environment-friendly seed coating agent for maize and researches its mechanism of action. The natural polysaccharide polymer, which is the main active ingredient of this environment-friendly seed coating agent, has the characteristics of innocuity and harmlessness, and it can replace the toxic ingredients used in traditional seed coating agents. This environment-friendly seed coating agent for maize was mainly made up of the natural polysaccharide polymer and other additives. The field trials results showed that the control efficacy of Helminthosporium maydis came to 93.72%, the anti-feeding rate of cutworms came to 81.29%, and the maize yield was increased by 17.75%. Besides, the LD 50 value (half the lethal dose in rats) of this seed coating agent was 10 times higher than that of the traditional seed coating agents. This seed coating agent could improve the activity of plant protective enzymes (peroxidase, catalase and superoxidase dismutase) and increase the chlorophyll content. This seed coating agent has four characteristics of disease prevention, desinsectization, increasing yield and safety. Results of mechanism analyses showed that this seed coating agent could enhance disease control effectiveness by improving plant protective enzymes activity and increase maize yield by improving chlorophyll content. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

The ethyl acetate fraction of corn silk exhibits dual antioxidant and anti-glycation activities and protects insulin-secreting cells from glucotoxicity.

PubMed

Chang, Chia-Chuan; Yuan, Wei; Roan, Hsiao-Yuh; Chang, Jia-Ling; Huang, Hsiu-Chen; Lee, Yu-Ching; Tsay, Huey Jen; Liu, Hui-Kang

2016-11-03

In this study, we aimed to develop a Stigmata Maydis (corn silk) fraction with dual bio-activities against oxidative stress and protein glycation to protect β-cells from diabetes-induced failure. Corn silk fractions were prepared by partition and chemically characterised by thin-layer chromatography. Free radical scavenging assay, glycation assay, and cell-based viability test (neutral red) were employed to decide the best fraction. Cell death analysis was executed by annexin V/ Propidium iodide staining. Cell proliferation was measured by WST-1. Finally, β-cell function was evaluated by β-cell marker gene expression (RT-PCR) and acute insulin secretion test. Four corn silk fractions were prepared from an ethanolic crude extract of corn silk. In vitro assays indicate ethyl acetate fraction (YMS-EA) was the most potent fraction. YMS-EA also attenuated the hydrogen peroxide- or methylglyoxal-induced induction of reactive oxygen species, reduction of cell viability, and inhibition of cell proliferation. However, YMS-EA was unable to prevent hydrogen peroxide-induced apoptosis or advanced glycation end-products-induced toxicity. Under hyperglycemic conditions, YMS-EA effectively reduced ROS levels, improved mRNA expression of insulin, glucokinase, and PDX-1, and enhanced glucose-stimulated insulin secretion. The similarity of bioactivities among apigenin, luteolin, and YMS-EA indicated that dual activities of YMS-EA might be derived from those compounds. We concluded that YMS-EA fraction could be developed as a preventive food agent against the glucotoxicity to β-cells in Type 2 diabetes.

Levels of some microelements and essential heavy metals in herbal teas in Serbia.

PubMed

Mihaljev, Zeljko; Zivkov-Balos, Milica; Cupić, Zeljko; Jaksić, Sandra

2014-01-01

Levels of Fe, Mn, Cu, Zn, Mo, Co, Ni, Se, Sn and Al were determined in 14 medicinal plants from Serbia, which are widely used in phytopharmacy as herbal teas. The following plants were investigated: yarrow (Achillea millefolium L.), basil (Ocimum hasilicum L.), St. John's wort (Hypericum perforatum L.), peppermint (Mentha x piperita L.), field horsetail (Equisetum arvense L.), stinging nettle (Urtica dioica L.), thyme (Thymus serpyllum L.), maize silk (Zea mays L. - Maydis stigma), hibiscus (Hibiscus sabdariffa L.), marshmallow (Althaea officinalis L.), chamomile (Matricaria chamomilla L.), rosehip/dog rose (Rosa canina L.), winter savory (Satureja montana L.) and spearmint (Mentha spicata L.). A total of 16 samples of different parts of medicinal plants (root, leaf, flower, herba) were examined, whereby 13 samples were delivered in original package and three samples were loose leaf herbs. Samples were prepared using the microwave digestion technique, and measurements were performed applying the atomic absorption spectrometry and mass spectrometry with inductively coupled plasma. Contents of microelements in the examined samples were in the range: Mn (23.86 - 453.71 mg/kg); Fe (61.87 - 673.0 mg/kg); Cu (6.68 - 24.46 mg/kg); Zn (16.11 - 113.81 mg/kg); Mo (0.576 - 4.265 mg/kg); Co (0.039 - 0.532 mg/kg); Se (0.036 - 0.146 mg/kg); Ni (0.738 - 6.034 mg/kg); Al (154.0 - 3015.0 mg/kg) and Sn (2.68 - 10.22 mg/kg). According to determined amounts of microelements, the investigated samples of herbal teas are considered safe for human consumption.

Assessment of fungal diversity in a water-damaged office building.

PubMed

Green, Brett J; Lemons, Angela R; Park, Yeonmi; Cox-Ganser, Jean M; Park, Ju-Hyeong

2017-04-01

Recent studies have described fungal communities in indoor environments using gene sequencing-based approaches. In this study, dust-borne fungal communities were elucidated from a water-damaged office building located in the northeastern region of the United States using internal transcribed spacer (ITS) rRNA gene sequencing. Genomic DNA was extracted from 5 mg of floor dust derived from 22 samples collected from either the lower floors (n = 8) or a top floor (n = 14) of the office building. ITS gene sequencing resolved a total of 933 ITS sequences and was clustered into 216 fungal operational taxonomic units (OTUs). Analysis of fungal OTUs at the 97% similarity threshold showed a difference between the lower and top floors that was marginally significant (p = 0.049). Species richness and diversity indices were reduced in the lower floor samples compared to the top floor samples and there was a high degree of compositional dissimilarity within and between the two different areas within the building. Fungal OTUs were placed in the phyla Ascomycota (55%), Basidiomycota (41%), Zygomycota (3%), Glomeromycota (0.4%), Chytridiomycota (0.3%), and unassigned fungi (0.5%). The Ascomycota classes with the highest relative abundances included the Dothideomycetes (30%) and Eurotiomycetes (16%). The Basidiomycota consisted of the classes Ustilaginomycetes (14%), Tremellomycetes (11%), and Agaricomycetes (8%). Sequence reads derived from the plant pathogen Ustilago syntherismae were the most abundant in the analysis as were obligate Basidiomycota yeast species that accounted for 12% and 11% of fungal ITS sequences, respectively. ITS gene sequencing provides additional insight into the diversity of fungal OTUs. These data further highlight the contribution of fungi placed in the phylum Basidiomycota, obligate yeasts, as well as xerophilic species that are typically not resolved using traditional culture methods.

Fungal spores in four catholic churches in the metropolitan area of Monterrey, Nuevo León State, Mexico--First study.

PubMed

Estrada, Alejandra Rocha; Torres, Elizabeth Molina; Vázquez, Marco Antonio Alvarado; Piñero, Jorge Luis Hernandez; Lucio, Marco Antonio Guzmán; Martínez, Sergio Manuel Salcedo

2015-01-01

About 500,000 species of fungi have been described to-date, although an estimated between 1 - 1.5 million species may occur. They have a wide distribution in nature, contributing to the decomposition of organic matter and playing a part in the biogeochemical cycles of major nutrients. A small number are considered pathogens of animals and plants. There is ample historical evidence that certain types of allergies are associated with fungi; exposure to fungal allergens occurs in both outdoor and indoor spaces. Many indoor allergens are the same as those found outside buildings, entering through windows and doors, ventilation systems, or through cracks or other fissures in the walls. To determine the diversity and abundance of fungal spores inside four churches in the metropolitan area of Monterrey city in Mexico. The study was carried out from July 2009 - January 2010 using a Hirst type volumetric collector (Burkard Manufacturing Co Ltd). A total of 31,629 spores from 54 taxa were registered in the four churches. The building that showed the highest amount of spores was the Santa Catarina Mártir Church with 12,766 spores, followed by Cristo Rey with 7,155 and Nuestra Señora del Roble with 6,887. Regularly high concentrations of spores were recorded from 14:00 - 20:00 hours. The highest concentration value was observed at the church of Santa Catarina Mártir at 16:00 hours with 1153 spores/m 3 air. The most abundant spores in the four churches studied corresponded to Cladosporium, the Aspergillus/Penicillium complex, Coprinus, Ganoderma, Curvularia and Ustilago.

Mrt, a Gene Unique to Fungi, Encodes an Oligosaccharide Transporter and Facilitates Rhizosphere Competency in Metarhizium robertsii1[C][W

PubMed Central

Fang, Weiguo; St. Leger, Raymond J.

2010-01-01

The symbiotic associations between rhizospheric fungi and plants have enormous environmental impact. Fungi are crucial to plant health as antagonists of pathogens and herbivores and facilitate the uptake of soil nutrients. However, little is known about the plant products obtained by fungi in exchange or how they are transported through the symbiotic interface. Here, we demonstrate that sucrose and raffinose family oligosaccharides in root exudates are important for rhizosphere competence in the insect pathogen Metarhizium robertsii (formerly known as Metarhizium anisopliae). We identified mutants in the Metarhizium raffinose transporter (Mrt) gene of M. robertsii that grew poorly in root exudate and were greatly reduced in rhizosphere competence on grass roots. Studies on sugar uptake, including competition assays, revealed that MRT was a sucrose and galactoside transporter. Disrupting MRT resulted in greatly reduced or no growth on sucrose and galactosides but did not affect growth on monosaccharides or oligosaccharides composed entirely of glucose subunits. Consistent with this, expression of Mrt is exclusively up-regulated by galactosides and sucrose. Expressing a green fluorescent protein gene under the control of the Mrt promoter confirmed that MRT was expressed by germlings in the vicinity of grass roots but not in surrounding bulk soil. Disrupting Mrt did not reduce virulence to insects, demonstrating that Mrt is exclusively involved in M. robertsii’s interactions with plants. To our knowledge, MRT is the first oligosaccharide transporter identified and characterized in a fungus and is unique to filamentous fungi, but homologous genes in Magnaporthe, Ustilago, Aspergillus, Fusarium, Epichloe, and Penicillium species indicate that oligosaccharide transport is of widespread significance. PMID:20837701

Marker-assisted introgression of opaque2 allele for rapid conversion of elite hybrids into quality protein maize.

PubMed

Hossain, Firoz; Muthusamy, Vignesh; Pandey, Neha; Vishwakarma, Ashish K; Baveja, Aanchal; Zunjare, Rajkumar U; Thirunavukkarasu, Nepolean; Saha, Supradip; Manjaiah, Kanchikeri M Manjaiah; Prasanna, Boddupalli M; Gupta, Hari S

2018-03-01

Maize is a valuable source of food and feed worldwide. Maize endosperm protein is, however nutritionally poor due to the reduced levels of two essential amino acids, lysine and tryptophan. In this study, recessive opaque2 (o2) allele that confers enhanced endosperm lysine and tryptophan, was introgressed using marker-assisted backcross breeding into three normal inbred lines (HKI323, HKI1105 and HKI1128). These are the parental lines of three popular medium-maturing single cross hybrids (HM4, HM8 and HM9) in India. Gene-based simple sequence repeat (SSR) markers (umc1066 and phi057) were successfully deployed for introgression of o2 allele. Background selection using genome-based SSRs helped in recovering > 96% of recurrent parent genome. The newly developed quality protein maize (QPM) inbreds showed modified kernels (25-50% opaqueness) coupled with high degree of phenotypic resemblance to the respective recipient lines, including grain yield. In addition, endosperm protein quality showed increased lysine and tryptophan in the inbreds to the range of 52-95% and 47-118%, respectively. The reconstituted QPM hybrids recorded significant enhancement of endosperm lysine (48-74%) and tryptophan (55-100%) in the endosperm. The QPM hybrids exhibited high phenotypic similarity with the original hybrids for morphological and yield contributing traits along with responses to some major diseases like turcicum leaf blight and maydis leaf blight. The grain yield of QPM hybrids was at par with their original versions under multilocation testing. These elite, high-yielding QPM hybrids with improved protein quality have been released and notified for commercial cultivation, and hold significant promise for improving nutritional security.

Fungal Endophyte Diversity and Bioactivity in the Indian Medicinal Plant Ocimum sanctum Linn

PubMed Central

Chowdhary, Kanika; Kaushik, Nutan

2015-01-01

Endophytic mycopopulation isolated from India’s Queen of herbs Tulsi (Ocimum sanctum) were explored and investigated for their diversity and antiphytopathogenic activity against widespread plant pathogens Botrytis cinerea, Sclerotinia sclerotiorum, Rhizoctonia solani and Fusarium oxysporum. 90 fungal isolates, representing 17 genera were recovered from 313 disease-free and surface sterilised plant segments (leaf and stem tissues) from three different geographic locations (Delhi, Hyderabad and Mukteshwar) during distinct sampling times in consequent years 2010 and 2011 in India. Fungal endophytes were subjected to molecular identification based on rDNA ITS sequence analysis. Plant pathogens such as F. verticillioides, B. maydis, C. coarctatum, R. bataticola, Hypoxylon sp., Diaporthe phaseolorum, Alternaria tenuissima and A. alternata have occurred as endophyte only during second sampling (second sampling in 2011) in the present study. Bi-plot generated by principal component analysis suggested tissue specificity of certain fungal endophytes. Dendrogram revealed species abundance as a function of mean temperature of the location at the time of sampling. Shannon diversity in the first collection is highest in Hyderabad leaf tissues (H' = 1.907) whereas in second collection it was highest from leaf tissues of Delhi (H' = 1.846). Mukteshwar (altitude: 7500 feet) reported least isolation rate in second collection. Nearly 23% of the total fungal isolates were considered as potent biocontrol agent. Hexane extract of M. phaseolina recovered from Hyderabad in first collection demonstrated highest activity against S. sclerotiorum with IC50 value of 0.38 mg/ml. Additionally, its components 2H-pyran-2-one, 5,6-dihydro-6-pentyl and palmitic acid, methyl ester as reported by GC-MS Chromatogram upon evaluation for their antiphytopathogenic activity exhibited IC50 value of 1.002 and 0.662 against respectively S. sclerotiorum indicating their significant role in antiphytopathogenic activity of hexane extract. The production of 2H-pyran-2-one, 5,6-dihydro-6-pentyl from M. phaseolina, an endophytic fungus is being reported for the first time. PMID:26529087

Traditionally used medicinal plants against uncomplicated urinary tract infections: Are unusual, flavan-4-ol- and derhamnosylmaysin derivatives responsible for the antiadhesive activity of extracts obtained from stigmata of Zea mays L. against uropathogenic E. coli and Benzethonium chloride as frequent contaminant faking potential antibacterial activities?

PubMed

Rafsanjany, Nasli; Sendker, Jandirk; Lechtenberg, Matthias; Petereit, Frank; Scharf, Birte; Hensel, Andreas

2015-09-01

The dried stigmata from Zea mays L. are used traditionally for the treatment of uncomplicated urinary tract infections. A recent screening has indicated that hydroalcoholic extract of the herbal material inhibits the adhesion of uropathogenic Escherichia coli (UPEC) to T24 bladder cells. For verification of these data EtOH-water (1:1) extracts from 4 different batches of Maydis stigmata were investigated. Within an in vitro adhesion assay (UPEC strain 2980 and human T24 bladder cells) a dose-dependent antiadhesive activity against UPEC was verified (IC50 1040μg/mL). Bioassay guided fractionation of M. stigmata, batch S1, by EtOH-water extraction, followed by chromatography on Sephadex LH20 revealed two active fractions (I and XI). Further purification of fraction I and structure elucidation of the isolated compound revealed the presence of significant amounts of the biocide benzethonium chloride as contaminant. Benzethonium chloride was also identified in subsequent investigations in 2 different batches of M. stigmata. The presence of such nondeclared and illegal contaminants in the herbal raw material market has to be discussed intensively. From benzethonium-free raw material (batch S2) as well as from batch S1 fraction XI was further fractionated by MPLC and preparative HPLC, leading to a still complex subfraction XIG, which was analyzed by UHPLC/+ESI-QTOF-MS analysis. Advanced data processing and species-metabolite relationship database revealed the tentatively existence of the unusual C-glycosidic flavones derhamnosylmaysin (6), 3'-deoxyrhamnosylmaysin (4), 3'-O-methylderhamnosylmaysin (3), apiferol (2) and alternanthin (8) which might be related to the antiadhesive activity of this subfraction against UPEC. Copyright © 2015 Elsevier B.V. All rights reserved.

Transformation in fungi.

PubMed Central

Fincham, J R

1989-01-01

Transformation with exogenous deoxyribonucleic acid (DNA) now appears to be possible with all fungal species, or at least all that can be grown in culture. This field of research is at present dominated by Saccharomyces cerevisiae and two filamentous members of the class Ascomycetes, Aspergillus nidulans and Neurospora crassa, with substantial contributions also from fission yeast (Schizosaccharomyces pombe) and another filamentous member of the class Ascomycetes, Podospora anserina. However, transformation has been demonstrated, and will no doubt be extensively used, in representatives of most of the main fungal classes, including Phycomycetes, Basidiomycetes (the order Agaricales and Ustilago species), and a number of the Fungi Imperfecti. The list includes a number of plant pathogens, and transformation is likely to become important in the analysis of the molecular basis of pathogenicity. Transformation may be maintained either by using an autonomously replicating plasmid as a vehicle for the transforming DNA or through integration of the DNA into the chromosomes. In S. cerevisiae and other yeasts, a variety of autonomously replicating plasmids have been used successfully, some of them designed for use as shuttle vectors for Escherichia coli as well as for yeast transformation. Suitable plasmids are not yet available for use in filamentous fungi, in which stable transformation is dependent on chromosomal integration. In Saccharomyces cerevisiae, integration of transforming DNA is virtually always by homology; in filamentous fungi, in contrast, it occurs just as frequently at nonhomologous (ectopic) chromosomal sites. The main importance of transformation in fungi at present is in connection with gene cloning and the analysis of gene function. The most advanced work is being done with S. cerevisiae, in which the virtual restriction of stable DNA integration to homologous chromosome loci enables gene disruption and gene replacement to be carried out with greater precision and efficiency than is possible in other species that show a high proportion of DNA integration events at nonhomologous (ectopic) sites. With a little more trouble, however, the methodology pioneered for S. cerevisiae can be applied to other fungi too. Transformation of fungi with DNA constructs designed for high gene expression and efficient secretion of gene products appears to have great commercial potential. PMID:2651864

Assessing Performance of Spore Samplers in Monitoring Aeromycobiota and Fungal Plant Pathogen Diversity in Canada.

PubMed

Chen, Wen; Hambleton, Sarah; Seifert, Keith A; Carisse, Odile; Diarra, Moussa S; Peters, Rick D; Lowe, Christine; Chapados, Julie T; Lévesque, C André

2018-05-01

Spore samplers are widely used in pathogen surveillance but not so much for monitoring the composition of aeromycobiota. In Canada, a nationwide spore-sampling network (AeroNet) was established as a pilot project to assess fungal community composition in air and rain samples collected using three different spore samplers in the summers of 2010 and 2011. Metabarcodes of the internal transcribed spacer (ITS) were exhaustively characterized for three of the network sites, in British Columbia (BC), Québec (QC), and Prince Edward Island (PEI), to compare performance of the samplers. Sampler type accounted for ca. 20% of the total explainable variance in aeromycobiota compositional heterogeneity, with air samplers recovering more Ascomycota and rain samplers recovering more Basidiomycota. Spore samplers showed different abilities to collect 27 fungal genera that are plant pathogens. For instance, Cladosporium spp., Drechslera spp., and Entyloma spp. were collected mainly by air samplers, while Fusarium spp., Microdochium spp., and Ustilago spp. were recovered more frequently with rain samplers. The diversity and abundance of some fungi were significantly affected by sampling location and time (e.g., Alternaria and Bipolaris ) and weather conditions (e.g., Mycocentrospora and Leptosphaeria ), and depended on using ITS1 or ITS2 as the barcoding region (e.g., Epicoccum and Botrytis ). The observation that Canada's aeromycobiota diversity correlates with cooler, wetter conditions and northward wind requires support from more long-term data sets. Our vision of the AeroNet network, combined with high-throughput sequencing (HTS) and well-designed sampling strategies, may contribute significantly to a national biovigilance network for protecting plants of agricultural and economic importance in Canada. IMPORTANCE The current study compared the performance of spore samplers for collecting broad-spectrum air- and rain-borne fungal pathogens using a metabarcoding approach. The results provided a thorough characterization of the aeromycobiota in the coastal regions of Canada in relation to the influence of climatic factors. This study lays the methodological basis to eventually develop knowledge-based guidance on pest surveillance by assisting in the selection of appropriate spore samplers. © Crown copyright 2018.

[Atmospheric concentration of fungus spores in Ankara and the effect of meteorological factors in 2003 period].

PubMed

Ceter, Talip; Pinar, Nur Münevver

2009-10-01

The atmospheric concentrations of airborne fungus spores change continuously according to the meteorological factors, and their intensity have important allergic effects on atopic subjects and opportunistic pathogenic effects on immunocompromised patients. The aim of this study was to identify the fungal spores found in Ankara atmosphere during 2003 period and to investigate the changes in spore concentrations in relation to meteorological factors. Fungal spores were sampled by using 7-day Burkard volumetric trap between January to December 2003, and probable identification was performed microscopically based on their morphological structures. A total of 433.079 spores/m3 belonging to 35 taxa were observed during the study. The rates of these taxa were as follows; 75.5% Cladosporium, 6.1% Alternaria, 2.2% Leptosphaeria, 2.2% Ustilago, 2.1% 1-septate ascospores, 2% Exosporium, 1.6% Pleospora, and 1.3% Drechslera. The other taxa with concentrations < 1% have consisted a total of 7.1% of all atmospheric spores (Puccinia, Curvularia, Coprinus, Nigrospora, Periconia, Melanomma, Torula, Ascobolus, Agrocybe, Pithomyces, Stemphyllium, Ganoderma, Boletus, Peronospora, Venturia, Paraphaeosphaeria, Epicoccum, Didymella, Chaetomium and Fusarium rates between 0.7-0.1%; Oidium, Xylaria, Botrytis, Melanospora, Dictyosporium, Sporormiella and Tetracoccosporium rates between 0.09-0.01%). Although fungal spores were detected in all months in Ankara atmosphere, the evaluation of the seasonal distribution of spore concentrations revealed that the highest value was detected in July (100.697 spores/m3), while the lowest value was in January (4268 spores/m3). When the effects of meteorological factors on spore concentrations were investigated, it was found that, monthly mean temperature (> 20 degrees C) has a strong positive correlation (p < 0.01), and monthly mean relative humidity (< %50) and precipitation (0-20 mm) have strong negative correlations (p < 0.01) on the spore concentrations, while wind velocity (3 m/s) has a slightly positive effect. An annual spore calendar which indicated weekly concentrations and allergenicity levels of those identified fungal spores, was also prepared in this study. In conclusion, it is expected that these data would be helpful for the researchers in the area of aeropalinology and for the clinicians to evaluate allergic diseases.

[A general review of the discussion at the Beijing International Symposium on Population and Development].

PubMed

Ren, Y

1985-03-29

A general review of papers and discussions at the Beijing International Symposium on Population and Development held December 10-14, 1984 is presented. Discussions on population and development included China's population change 1949-1982, impacts of economic change on Tianjin's population, the population factor in economic development policy-making, Japanese population and development, recent population development in Hungary, population and economy, comprehensive long-term population development in Russia, fertility rate change factors in China, Shanghai's population change, and population and economic development in Mian County, Shaanxi Province. Fertility rate changes were discussed, including multinational borderline value assumptions, recent trends in life span fertility rate in China, fertility rate in Jiangsu Province, fertility rate change in Zhejiang Province, and sterilization in Yangjiaping, Thailand. Population and employment discussions included the economic impact of world population change, the 1984 International Population Conference, changes in economically productive population and employment strategy, employed/unemployed populations in Guangdong Province, and the economic composition of China's population. Urbanization discussions covered population and development methodological problems, population growth and economic development in the Pacific region, surplus rural population transfer and economic development in China, urbanization analysis, trends and urban population distribution problems, and Laioning Province population development. Issues in migration, population distribution, and regional population included migration and development of the Great Northwest, internal migration to Beijing, Chinese population growth and economic development by major region, and current population changes of Chinese Tibetans. Under social problems of population, discussions included women's status, development and population change, Shanghai's aging trend, analysis of the aged population, analysis of educational quality in Anhui Province, and the retirement system in Chinese villages.

Population demographics and genetic diversity in remnant and translocated populations of sea otters

USGS Publications Warehouse

Bodkin, James L.; Ballachey, Brenda E.; Cronin, M.A.; Scribner, K.T.

1999-01-01

The effects of small population size on genetic diversity and subsequent population recovery are theoretically predicted, but few empirical data are available to describe those relations. We use data from four remnant and three translocated sea otter (Enhydra lutris) populations to examine relations among magnitude and duration of minimum population size, population growth rates, and genetic variation. Metochondrial (mt)DNA haplotype diversity was correlated with the number of years at minimum population size (r = -0.741, p = 0.038) and minimum population size (r = 0.709, p = 0.054). We found no relation between population growth and haplotype diversity, altough growth was significantly greater in translocated than in remnant populations. Haplotype diversity in populations established from two sources was higher than in a population established from a single source and was higher than in the respective source populations. Haplotype frequencies in translocated populations of founding sizes of 4 and 28 differed from expected, indicating genetic drift and differential reproduction between source populations, whereas haplotype frequencies in a translocated population with a founding size of 150 did not. Relations between population demographics and genetic characteristics suggest that genetic sampling of source and translocated populations can provide valuable inferences about translocations.

World Population: Facts in Focus. World Population Data Sheet Workbook. Population Learning Series.

ERIC Educational Resources Information Center

Crews, Kimberly A.

This workbook teaches population analysis using world population statistics. To complete the four student activity sheets, the students refer to the included "1988 World Population Data Sheet" which lists nations' statistical data that includes population totals, projected population, birth and death rates, fertility levels, and the…

Population inertia and its sensitivity to changes in vital rates and population structure

USGS Publications Warehouse

Koons, David N.; Holmes, Randall R.; Grand, James B.

2007-01-01

Because the (st)age structure of a population may rarely be stable, studies of transient population dynamics and population momentum are becoming ever more popular. Yet, studies of "population momentum" are restricted in the sense that they describe the inertia of population size resulting from a demographic transition to the stationary population growth rate. Although rarely mentioned, inertia in population size is a general phenomenon and can be produced by any demographic transition or perturbation. Because population size is of central importance in demography, conservation, and management, formulas relating the sensitivity of population inertia to changes in underlying vital rates and population structure could provide much-needed insight into the dynamics of populations with unstable (st)age structure. Here, we derive such formulas, which are readily computable, and provide examples of their potential use in studies of life history and applied arenas of population study. ?? 2007 by the Ecological Society of America.

Regarding the confusion between the population concept and Mayr's "population thinking".

PubMed

Hey, Jody

2011-12-01

Ernst Mayr said that one of Darwin's greatest contributions was to show scholars the way to population thinking, and to help them discard a mindset of typological thinking. Population thinking rejects a focus on a central representative type, and emphasizes the variation among individuals. However, Mayr's choice of terms has led to confusion, particularly among biologists who study natural populations. Both population thinking and the concept of a biological population were inspired by Darwin, and from Darwin the chain for both concepts runs through Francis Galton who introduced the statistical usage of "population" that appears in Mayr's population thinking. It was Galton's "population" that was modified by geneticists and biometricians in the early 20th century to refer to an interbreeding and evolving community of organisms. Under this meaning, a population is a biological entity and so paradoxically population thinking, which emphasizes variation at the expense of dwelling on entities, is usually not about populations. Mayr did not address the potential for misunderstanding but for him the important part of the population concept was that the organisms within a population were variable, and so he probably thought there should not be confusion between population thinking and the concept of a population.

Strong fluctuations in aboveground population size do not limit genetic diversity in populations of an endangered biennial species.

PubMed

Münzbergová, Zuzana; Šurinová, Maria; Husáková, Iveta; Brabec, Jiří

2018-04-26

Assessing genetic diversity within populations of rare species and understanding its determinants are crucial for effective species protection. While a lot is known about the relationships between genetic diversity, fitness, and current population size, very few studies explored the effects of past population size. Knowledge of past population size may, however, improve our ability to predict future population fates. We studied Gentianella praecox subsp. bohemica, a biennial species with extensive seed bank. We tested the effect of current, past minimal and maximal population size, and harmonic mean of population sizes within the last 15 years on genetic diversity and fitness. Maximum population size over the last 15 years was the best predictor of expected heterozygosity of the populations and was significantly related to current population size and management. Plant fitness was significantly related to current as well as maximum population size and expected heterozygosity. The results suggested that information on past population size may improve our understanding of contemporary genetic diversity across populations. They demonstrated that despite the strong fluctuations in population size, large reductions in population size do not result in immediate loss of genetic diversity and reduction of fitness within the populations. This is likely due to the seed bank of the species serving as reservoir of the genetic diversity of the populations. From a conservation point of view, this suggests that the restoration of small populations of short-lived species with permanent seed bank is possible as these populations may still be genetically diverse.

Demographic and genetic status of an isolated population of bog turtles (Glyptemys muhlenbergii): Implications for managing small populations of long-lived animals

USGS Publications Warehouse

Pittman, Shannon E.; King, T.L.; Faurby, S.; Dorcas, M.E.

2011-01-01

In this study, we sought to determine the population stability and genetic diversity of one isolated population of the federally-threatened bog turtle (Glyptemys muhlenbergii) in North Carolina. Using capture-recapture data, we estimated adult survival and population growth rate from 1992 to 2007. We found that the population decreased from an estimated 36 adult turtles in 1994 to approximately 11 adult turtles in 2007. We found a constant adult survival of 0. 893 (SE = 0. 018, 95% confidence interval, 0. 853-0. 924) between 1992 and 2007. Using 18 microsatellite markers, we compared the genetic status of this population with five other bog turtle populations. The target population displayed allelic richness (4. 8 ?? 0. 5) and observed heterozygosity (0. 619 ?? 0. 064) within the range of the other bog turtle populations. Coalescent analysis of population growth rate, effective population size, and timing of population structuring event also indicated the genetics of the target population were comparable to the other populations studied. Estimates of effective population size were a proportion of the census size in all populations except the target population, in which the effective population size was larger than the census size (30 turtles vs. 11 turtles). We attribute the high genetic diversity in the target population to the presence of multiple generations of old turtles. This study illustrates that the demographic status of populations of long-lived species may not be reflected genetically if a decline occurred recently. Consequently, the genetic integrity of populations of long-lived animals experiencing rapid demographic bottlenecks may be preserved through conservation efforts effective in addressing demographic problems. ?? 2011 Springer Science+Business Media B.V.

Effects of spatial structure of population size on the population dynamics of barnacles across their elevational range.

PubMed

Fukaya, Keiichi; Okuda, Takehiro; Nakaoka, Masahiro; Noda, Takashi

2014-11-01

Explanations for why population dynamics vary across the range of a species reflect two contrasting hypotheses: (i) temporal variability of populations is larger in the centre of the range compared to the margins because overcompensatory density dependence destabilizes population dynamics and (ii) population variability is larger near the margins, where populations are more susceptible to environmental fluctuations. In both of these hypotheses, positions within the range are assumed to affect population variability. In contrast, the fact that population variability is often related to mean population size implies that the spatial structure of the population size within the range of a species may also be a useful predictor of the spatial variation in temporal variability of population size over the range of the species. To explore how population temporal variability varies spatially and the underlying processes responsible for the spatial variation, we focused on the intertidal barnacle Chthamalus dalli and examined differences in its population dynamics along the tidal levels it inhabits. Changes in coverage of barnacle populations were monitored for 10.5 years at 25 plots spanning the elevational range of this species. Data were analysed by fitting a population dynamics model to estimate the effects of density-dependent and density-independent processes on population growth. We also examined the temporal mean-variance relationship of population size with parameters estimated from the population dynamics model. We found that the relative variability of populations tended to increase from the centre of the elevational range towards the margins because of an increase in the magnitude of stochastic fluctuations of growth rates. Thus, our results supported hypothesis (2). We also found that spatial variations in temporal population variability were well characterized by Taylor's power law, the relative population variability being inversely related to the mean population size. Results suggest that understanding the population dynamics of a species over its range may be facilitated by taking the spatial structure of population size into account as well as by considering changes in population processes as a function of position within the range of the species. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

76 FR 17620 - Census Advisory Committees

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-30

... African American Population, the American Indian and Alaska Native Populations, the Asian Population, the... American Population, the American Indian and Alaska Native Populations, the Asian Population, the Hispanic...

76 FR 56395 - Census Advisory Committees

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-13

... African American Population, the American Indian and Alaska Native Populations, the Asian Population, the... American Population, the American Indian and Alaska Native Populations, the Asian Population, the Hispanic...

Allee effect: the story behind the stabilization or extinction of microbial ecosystem.

PubMed

Goswami, Madhurankhi; Bhattacharyya, Purnita; Tribedi, Prosun

2017-03-01

A population exhibiting Allee effect shows a positive correlation between population fitness and population size or density. Allee effect decides the extinction or conservation of a microbial population and thus appears to be an important criterion in population ecology. The underlying factor of Allee effect that decides the stabilization and extinction of a particular population density is the threshold or the critical density of their abundance. According to Allee, microbial populations exhibit a definite, critical or threshold density, beyond which the population fitness of a particular population increases with the rise in population density and below it, the population fitness goes down with the decrease in population density. In particular, microbial population displays advantageous traits such as biofilm formation, expression of virulence genes, spore formation and many more only at a high population density. It has also been observed that microorganisms exhibiting a lower population density undergo complete extinction from the residual microbial ecosystem. In reference to Allee effect, decrease in population density or size introduces deleterious mutations among the population density through genetic drift. Mutations are carried forward to successive generations resulting in its accumulation among the population density thus reducing its microbial fitness and thereby increasing the risk of extinction of a particular microbial population. However, when the microbial load is high, the chance of genetic drift is less, and through the process of biofilm formation, the cooperation existing among the microbial population increases that increases the microbial fitness. Thus, the high microbial population through the formation of microbial biofilm stabilizes the ecosystem by increasing fitness. Taken together, microbial fitness shows positive correlation with the ecosystem conservation and negative correlation with ecosystem extinction.

Genetic diversity of populations and clones of Rhopilema esculentum in China based on AFLP analysis

NASA Astrophysics Data System (ADS)

Qiao, Hongjin; Liu, Xiangquan; Zhang, Xijia; Jiang, Haibin; Wang, Jiying; Zhang, Limin

2013-03-01

Amplified fragment length polymorphisms (AFLP) markers were developed to assess the genetic variation of populations and clones of Rhopilema esculentum Kishinouye (Scyphozoa, Rhizostomatidae). One hundred and seventy-nine loci from 56 individuals of two hatchery populations and two wild populations were genotyped with five primer combinations. The polymorphic ratio, Shannon's diversity index and average heterozygosity were 70.3%, 0.346 and 0.228 for the white hatchery population, 74.3%, 0.313, and 0.201 for the red hatchery population, 79.3%, 0.349, and 0.224 for the Jiangsu wild population, and 74.9%, 0.328 and 0.210 for the Penglai wild population, respectively. Thus, all populations had a relatively high level of genetic diversity. A specific band was identified that could separate the white from the red hatchery population. There was 84.85% genetic differentiation within populations. Individual cluster analysis using unweighted pair-group method with arithmetic mean (UPGMA) suggested that hatchery populations and wild populations could be divided. For the hatchery populations, the white and red populations clustered separately; however, for the wild populations, Penglai and Jiangsu populations clustered together. The genetic diversity at the clone level was also determined. Our data suggest that there are relatively high genetic diversities within populations but low genetic differentiation between populations, which may be related to the long-term use of germplasm resources from Jiangsu Province for artificial seeding and releasing. These findings will benefit the artificial seeding and conservation of the germplasm resources.

[The Marxist outlook on population].

PubMed

Qin, R

1984-09-29

Marxist population theory and world population are discussed. From his study of capitalist population theory Marx concluded, "In capitalist reproduction, poverty produces population," thus rejecting Malthusian population determinism theory and developing economic determinism. According to UN statistics, world population has stabilized since the middle of this century after having doubled every hundred years for the last 300; population in the developed countries showed a positive decrease and average net population growth of the developing countries also decreased. The premise of this paper is that population grows according to social economy development. During the last several hundred years, world wealth increased much faster than population; in the last 200 years alone, the population has increased fivefold, but wealth fortyfold. In addition, world population analysis reveals an inverse relationship between wealth and population in the developed and developing countries: the poorer the country, the greater the population. From this perspective, the study of population must begin with surplus labor. Accumulation of surplus production is the foundation of continuous social development and the basis for population growth. The major difference in methods between capitalist countries and China is that the capitalist-planned fertility affects the individual family while Chinese-planned fertility has the whole nation in mind. Human fertility is determined by the economic system. Private ownership determines the private nature of fertility and public ownership determines the public nature of fertility. Thus population development is determined by the accumulation of social wealth.

Does source population size affect performance in new environments?

PubMed Central

Yates, Matthew C; Fraser, Dylan J

2014-01-01

Small populations are predicted to perform poorly relative to large populations when experiencing environmental change. To explore this prediction in nature, data from reciprocal transplant, common garden, and translocation studies were compared meta-analytically. We contrasted changes in performance resulting from transplantation to new environments among individuals originating from different sized source populations from plants and salmonids. We then evaluated the effect of source population size on performance in natural common garden environments and the relationship between population size and habitat quality. In ‘home-away’ contrasts, large populations exhibited reduced performance in new environments. In common gardens, the effect of source population size on performance was inconsistent across life-history stages (LHS) and environments. When transplanted to the same set of new environments, small populations either performed equally well or better than large populations, depending on life stage. Conversely, large populations outperformed small populations within native environments, but only at later life stages. Population size was not associated with habitat quality. Several factors might explain the negative association between source population size and performance in new environments: (i) stronger local adaptation in large populations and antagonistic pleiotropy, (ii) the maintenance of genetic variation in small populations, and (iii) potential environmental differences between large and small populations. PMID:25469166

75 FR 13494 - Census Advisory Committees

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-22

... African American Population, the American Indian and Alaska Native Populations, the Asian Population, the... Populations, the Asian Population, the Hispanic Population, and the Native Hawaiian and Other Pacific Islander...

Introgression Makes Waves in Inferred Histories of Effective Population Size.

PubMed

Hawks, John

2017-01-01

Human populations have a complex history of introgression and of changing population size. Human genetic variation has been affected by both these processes, so inference of past population size depends upon the pattern of gene flow and introgression among past populations. One remarkable aspect of human population history as inferred from genetics is a consistent "wave" of larger effective population sizes, found in both African and non-African populations, that appears to reflect events prior to the last 100,000 years. I carried out a series of simulations to investigate how introgression and gene flow from genetically divergent ancestral populations affect the inference of ancestral effective population size. Both introgression and gene flow from an extinct, genetically divergent population consistently produce a wave in the history of inferred effective population size. The time and amplitude of the wave reflect the time of origin of the genetically divergent ancestral populations and the strength of introgression or gene flow. These results demonstrate that even small fractions of introgression or gene flow from ancient populations may have visible effects on the inference of effective population size.

Genetic Diversity and Structure of the Apiosporina morbosa Populations on Prunus spp.

PubMed

Zhang, Jinxiu; Fernando, W G Dilantha; Remphrey, William R

2005-08-01

ABSTRACT Populations of Apiosporina morbosa collected from 15 geographic locations in Canada and the United States and three host species, Prunus virginiana, P. pensylvanica, and P. padus, were evaluated using the sequence-related amplified polymorphism (SRAP) technique to determine their genetic diversity and population differentiation. Extensive diversity was detected in the A. morbosa populations, including 134 isolates from Canada and the United States, regardless of the origin of the population. The number of polymorphic loci varied from 6.9 to 82.8% in the geographic populations, and from 41.4 to 79.3% in the populations from four host genotypes based on 58 polymorphic fragments. In all, 44 to 100% of isolates in the geographic populations and 43.6 to 76.2% in populations from four host genotypes represented unique genotypes. Values of heterozygosity (H) varied from 2.8 to 28.3% in the geographic populations and 10.2 to 26.1% in the populations from four host genotypes. In general, the A. morbosa populations sampled from wild chokecherry showed a higher genetic diversity than those populations collected from other host species, whereas the populations isolated from cultivated chokecherry, P. virginiana 'Shubert Select', showed a reduction of genetic diversity compared with populations from wild P. virginiana. Significant population differentiation was found among both the geographic populations (P < 0.05) and populations from different host genotypes (P < 0.02). In the geographic populations, most of populations from cultivated and wild P. virginiana were closely clustered, and no population differentiation was detected except for the populations from Morris, Morden, and Winnipeg, Manitoba, Canada. Furthermore, the populations from P. virginiana in the same geographic locations had higher genetic identity and closer genetic distance to each other compared with those from different locations. Four populations from P. virginiana, P. pensylvanica, and P. padus, were significantly differentiated from each other (P < 0.02), except there was no differentiation between the Shubert Select and wild chokecherry populations (>P> = 0.334). Indirect estimation of gene flow showed that significant restricted gene flow existed between populations from different regions and host species. Gene flow rates (Nm) varied from <1 to 12.5, with higher gene flow rates among population pairs from the same host species (P = 1.000). The analysis of molecular variance revealed that a major genetic variance source came from the genetic variation among isolates within populations regardless of the origin and host genotype of the population. Although some locations had a limited number of isolates, the results of this study clearly showed that the genetic diversity and population differentiation of A. morbosa were closely associated with host genotypes and geographic locations, but mostly with the former.

40 CFR 68.30 - Defining offsite impacts-population.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 16 2014-07-01 2014-07-01 false Defining offsite impacts-population... impacts—population. (a) The owner or operator shall estimate in the RMP the population within a circle... defined in § 68.22(a). (b) Population to be defined. Population shall include residential population. The...

40 CFR 68.30 - Defining offsite impacts-population.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 16 2013-07-01 2013-07-01 false Defining offsite impacts-population... impacts—population. (a) The owner or operator shall estimate in the RMP the population within a circle... defined in § 68.22(a). (b) Population to be defined. Population shall include residential population. The...

40 CFR 68.30 - Defining offsite impacts-population.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 15 2011-07-01 2011-07-01 false Defining offsite impacts-population... impacts—population. (a) The owner or operator shall estimate in the RMP the population within a circle... defined in § 68.22(a). (b) Population to be defined. Population shall include residential population. The...

40 CFR 68.30 - Defining offsite impacts-population.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 16 2012-07-01 2012-07-01 false Defining offsite impacts-population... impacts—population. (a) The owner or operator shall estimate in the RMP the population within a circle... defined in § 68.22(a). (b) Population to be defined. Population shall include residential population. The...

Genetic health and population monitoring of two small black bear (Ursus americanus) populations in Alabama, with a regional perspective of genetic diversity and exchange

PubMed Central

Waits, Lisette P.; Adams, Jennifer R.; Seals, Christopher L.; Steury, Todd D.

2017-01-01

One of the major concerns in conservation today is the loss of genetic diversity which is a frequent consequence of population isolation and small population sizes. Fragmentation of populations and persecution of carnivores has posed a substantial threat to the persistence of free ranging carnivores in North America since the arrival of European settlers. Black bears have seen significant reductions in range size from their historic extent, which is most pronounced in the southeastern United States and even more starkly in Alabama where until recently bears were reduced to a single geographically isolated population in the Mobile River Basin. Recently a second population has naturally re-established itself in northeastern Alabama. We sought to determine size, genetic diversity and genetic connectivity for these two populations in relation to other regional populations. Both populations of black bears in Alabama had small population sizes and had moderate to low genetic diversity, but showed different levels of connectivity to surrounding populations of bears. The Mobile River Basin population had a small population size at only 86 individuals (76–124, 95% C.I.), the lowest genetic diversity of compared populations (richness = 2.33, Ho and He = 0.33), and showed near complete genetic isolation from surrounding populations across multiple tests. The newly recolonizing population in northeastern Alabama had a small but growing population doubling in 3 years (34 individuals 26–43, 95% C.I.), relatively moderate genetic diversity compared to surrounding populations (richness = 3.32, Ho = 0.53, He = 0.65), and showed a high level of genetic connectivity with surrounding populations. PMID:29117263

Variation of genetic diversity in a rapidly expanding population of the greater long-tailed hamster (Tscherskia triton) as revealed by microsatellites.

PubMed

Xu, Laixiang; Xue, Huiliang; Song, Mingjing; Zhao, Qinghua; Dong, Jingping; Liu, Juan; Guo, Yu; Xu, Tongqin; Cao, Xiaoping; Wang, Fusheng; Wang, Shuqing; Hao, Shushen; Yang, Hefang; Zhang, Zhibin

2013-01-01

Genetic diversity is essential for persistence of animal populations over both the short- and long-term. Previous studies suggest that genetic diversity may decrease with population decline due to genetic drift or inbreeding of small populations. For oscillating populations, there are some studies on the relationship between population density and genetic diversity, but these studies were based on short-term observation or in low-density phases. Evidence from rapidly expanding populations is lacking. In this study, genetic diversity of a rapidly expanding population of the Greater long-tailed hamsters during 1984-1990, in the Raoyang County of the North China Plain was studied using DNA microsatellite markers. Results show that genetic diversity was positively correlated with population density (as measured by % trap success), and the increase in population density was correlated with a decrease of genetic differentiation between the sub-population A and B. The genetic diversity tended to be higher in spring than in autumn. Variation in population density and genetic diversity are consistent between sub-population A and B. Such results suggest that dispersal is density- and season-dependent in a rapidly expanding population of the Greater long-tailed hamster. For typically solitary species, increasing population density can increase intra-specific attack, which is a driving force for dispersal. This situation is counterbalanced by decreasing population density caused by genetic drift or inbreeding as the result of small population size. Season is a major factor influencing population density and genetic diversity. Meanwhile, roads, used to be considered as geographical isolation, have less effect on genetic differentiation in a rapidly expanding population. Evidences suggest that gene flow (Nm) is positively correlated with population density, and it is significant higher in spring than that in autumn.

Genetic Diversity in Introduced Populations with an Allee Effect

PubMed Central

Wittmann, Meike J.; Gabriel, Wilfried; Metzler, Dirk

2014-01-01

A phenomenon that strongly influences the demography of small introduced populations and thereby potentially their genetic diversity is the demographic Allee effect, a reduction in population growth rates at small population sizes. We take a stochastic modeling approach to investigate levels of genetic diversity in populations that successfully overcame either a strong Allee effect, in which populations smaller than a certain critical size are expected to decline, or a weak Allee effect, in which the population growth rate is reduced at small sizes but not negative. Our results indicate that compared to successful populations without an Allee effect, successful populations with a strong Allee effect tend to (1) derive from larger founder population sizes and thus have a higher initial amount of genetic variation, (2) spend fewer generations at small population sizes where genetic drift is particularly strong, and (3) spend more time around the critical population size and thus experience more genetic drift there. In the case of multiple introduction events, there is an additional increase in diversity because Allee-effect populations tend to derive from a larger number of introduction events than other populations. Altogether, a strong Allee effect can either increase or decrease genetic diversity, depending on the average founder population size. By contrast, a weak Allee effect tends to decrease genetic diversity across the entire range of founder population sizes. Finally, we show that it is possible in principle to infer critical population sizes from genetic data, although this would require information from many independently introduced populations. PMID:25009147

Geographic distribution of genetic variation among native and introduced populations of Chinese tallow tree, Triadica sebifera (Euphorbiaceae).

PubMed

DeWalt, Saara J; Siemann, Evan; Rogers, William E

2011-07-01

Invasive plants often display genetically determined variation in patterns of growth and resource allocation between native and introduced genotypes, as well as among genotypes within different regions of the introduced range. We examined patterns of genetic variation within and among native and introduced populations of the tetraploid Chinese tallow tree (Triadica sebifera, Euphorbiaceae) to determine whether nonselective evolutionary processes or the introduction history could contribute to previously observed phenotypic differences between native and introduced populations as well as among introduced populations. We used six microsatellite markers to study 12 native populations in China, 51 introduced populations in the southeastern USA, and one introduced population in Australia. Genetic diversity was greater within and among native populations than introduced populations. Within the southeastern USA, populations in Georgia and South Carolina differed substantially in their genetic composition and had greater genetic diversity than the rest of the southeastern USA. Greater genetic similarity between some populations in the native range and introduced range indicate a common provenance for Georgia and South Carolina populations that could have come from any of several western or southern Chinese populations and a different provenance for other southeastern USA populations and the Australian population, which were most similar to more northeastern Chinese populations. Differences among introduced populations in potentially adaptive traits (e.g., herbivore tolerance, herbivore resistance, growth rates) may result in part from the introduction history, in particular from differences present among source populations in the native range.

Viability of the Alaskan breeding population of Steller’s eiders

USGS Publications Warehouse

Dunham, Kylee; Grand, James B.

2016-10-11

The U.S. Fish and Wildlife Service is tasked with setting objective and measurable criteria for delisting species or populations listed under the Endangered Species Act. Determining the acceptable threshold for extinction risk for any species or population is a challenging task, particularly when facing marked uncertainty. The Alaskan breeding population of Steller’s eiders (Polysticta stelleri) was listed as threatened under the Endangered Species Act in 1997 because of a perceived decline in abundance throughout their nesting range and geographic isolation from the Russian breeding population. Previous genetic studies and modeling efforts, however, suggest that there may be dispersal from the Russian breeding population. Additionally, evidence exists of population level nonbreeding events. Research was conducted to estimate population viability of the Alaskan breeding population of Steller’s eiders, using both an open and closed model of population process for this threatened population. Projections under a closed population model suggest this population has a 100 percent probability of extinction within 42 years. Projections under an open population model suggest that with immigration there is no probability of permanent extinction. Because of random immigration process and nonbreeding behavior, however, it is likely that this population will continue to be present in low and highly variable numbers on the breeding grounds in Alaska. Monitoring the winter population, which includes both Russian and Alaskan breeding birds, may offer a more comprehensive indication of population viability.

Inferring population structure and demographic history using Y-STR data from worldwide populations.

PubMed

Xu, Hongyang; Wang, Chuan-Chao; Shrestha, Rukesh; Wang, Ling-Xiang; Zhang, Manfei; He, Yungang; Kidd, Judith R; Kidd, Kenneth K; Jin, Li; Li, Hui

2015-02-01

The Y chromosome is one of the best genetic materials to explore the evolutionary history of human populations. Global analyses of Y chromosomal short tandem repeats (STRs) data can reveal very interesting world population structures and histories. However, previous Y-STR works tended to focus on small geographical ranges or only included limited sample sizes. In this study, we have investigated population structure and demographic history using 17 Y chromosomal STRs data of 979 males from 44 worldwide populations. The largest genetic distances have been observed between pairs of African and non-African populations. American populations with the lowest genetic diversities also showed large genetic distances and coancestry coefficients with other populations, whereas Eurasian populations displayed close genetic affinities. African populations tend to have the oldest time to the most recent common ancestors (TMRCAs), the largest effective population sizes and the earliest expansion times, whereas the American, Siberian, Melanesian, and isolated Atayal populations have the most recent TMRCAs and expansion times, and the smallest effective population sizes. This clear geographic pattern is well consistent with serial founder model for the origin of populations outside Africa. The Y-STR dataset presented here provides the most detailed view of worldwide population structure and human male demographic history, and additionally will be of great benefit to future forensic applications and population genetic studies.

Individualized population care: linking personal care to population care in general practice.

PubMed

Buetow, Stephen; Getz, Linn; Adams, Peter

2008-10-01

General practice is increasingly expected to deliver population care to individual patients. The feasibility and ethics of this policy shift have been challenged. Our aim is to suggest how to deliver population care while protecting personal care. We outline and discuss concepts of these types of care, their relation to the prevailing discourse regarding intervention benefits, and arguments for individualized population care. Individualized population care can enable general practice to meet the health targets of individual patients in the light of population-based goals. It unifies the concepts of personal care and whole population care. Personal care focuses on the individual good in particular consultations. Whole population care focuses on the overall health good of a population without reference to the individuality of each population member. These types of care constitute elements of a continuum that varies in purpose and objects of focus. The limitations of a crude dichotomy of personal care and population care are made explicit in a series of five arguments that lend support to the concept of individualized population care. We advocate a constructive but critical attitude towards the idea of population-based interventions in everyday general practice. Traditional personal care and whole population care can theoretically be integrated into individualized population care. However, this presupposes clinical-epidemiological expertise and moral awareness in practising clinicians.

Determining size and dispersion of minimum viable populations for land management planning and species conservation

NASA Astrophysics Data System (ADS)

Lehmkuhl, John F.

1984-03-01

The concept of minimum populations of wildlife and plants has only recently been discussed in the literature. Population genetics has emerged as a basic underlying criterion for determining minimum population size. This paper presents a genetic framework and procedure for determining minimum viable population size and dispersion strategies in the context of multiple-use land management planning. A procedure is presented for determining minimum population size based on maintenance of genetic heterozygosity and reduction of inbreeding. A minimum effective population size ( N e ) of 50 breeding animals is taken from the literature as the minimum shortterm size to keep inbreeding below 1% per generation. Steps in the procedure adjust N e to account for variance in progeny number, unequal sex ratios, overlapping generations, population fluctuations, and period of habitat/population constraint. The result is an approximate census number that falls within a range of effective population size of 50 500 individuals. This population range defines the time range of short- to long-term population fitness and evolutionary potential. The length of the term is a relative function of the species generation time. Two population dispersion strategies are proposed: core population and dispersed population.

A general methodology for population analysis

NASA Astrophysics Data System (ADS)

Lazov, Petar; Lazov, Igor

2014-12-01

For a given population with N - current and M - maximum number of entities, modeled by a Birth-Death Process (BDP) with size M+1, we introduce utilization parameter ρ, ratio of the primary birth and death rates in that BDP, which, physically, determines (equilibrium) macrostates of the population, and information parameter ν, which has an interpretation as population information stiffness. The BDP, modeling the population, is in the state n, n=0,1,…,M, if N=n. In presence of these two key metrics, applying continuity law, equilibrium balance equations concerning the probability distribution pn, n=0,1,…,M, of the quantity N, pn=Prob{N=n}, in equilibrium, and conservation law, and relying on the fundamental concepts population information and population entropy, we develop a general methodology for population analysis; thereto, by definition, population entropy is uncertainty, related to the population. In this approach, what is its essential contribution, the population information consists of three basic parts: elastic (Hooke's) or absorption/emission part, synchronization or inelastic part and null part; the first two parts, which determine uniquely the null part (the null part connects them), are the two basic components of the Information Spectrum of the population. Population entropy, as mean value of population information, follows this division of the information. A given population can function in information elastic, antielastic and inelastic regime. In an information linear population, the synchronization part of the information and entropy is absent. The population size, M+1, is the third key metric in this methodology. Namely, right supposing a population with infinite size, the most of the key quantities and results for populations with finite size, emerged in this methodology, vanish.

Development of Seven Microsatellite Markers Using Next Generation Sequencing for the Conservation on the Korean Population of Dorcus hopei (E. Saunders, 1854) (Coleoptera, Lucanidae)

PubMed Central

Kang, Tae Hwa; Han, Sang Hoon; Park, Sun Jae

2015-01-01

We developed microsatellite markers for genetic structural analyses of Dorcus hopei, a stag beetle species, using next generation sequencing and polymerase chain reaction (PCR)-based genotyping for regional populations. A total of 407,070,351 base pairs of genomic DNA containing >4000 microsatellite loci except AT repeats were sequenced. From 76 loci selected for primer design, 27 were polymorphic. Of these 27 markers, 10 were tested on three regional populations: two Chinese (Shichuan and Guangxi) and one Korean (Wanju). Three markers were excluded due to inconsistent amplification, genotyping errors, and Hardy-Weinberg equilibrium (HWE). By multi-locus genotyping, the allele number, observed heterozygosity and polymorphism information content of seven microsatellite loci were ranged 2‒10, 0.1333‒1.0000, and 0.1228‒0.8509, respectively. In an analysis on the genetic differentiation among regional populations including one Japanese population and one cross-breeding population, the individual colored bar-plots showed that both Chinese populations were closer to each other than to the Far East Asian populations. In Far East Asian populations, Wanju and Nirasaki populations could not be distinguished from each other because the frequency of genetic contents was very similar in some individuals of two populations. Moreover, the cross-breeding population contained all patterns of genetic contents shown in Chinese, Korean, and Japanese populations, compared with the genetic content frequency of each regional population. As a result, we examined whether the cross-breeding population might be a hybrid population, and might contain a possibility of interbreeding with Chinese populations in parental generations. Therefore, these markers will be useful for analyses of genetic diversity in populations, genetic relationships between regional populations, genetic structure analyses, and origin tests. PMID:26370965

Efficiency or equity? Simulating the impact of high-risk and population intervention strategies for the prevention of disease.

PubMed

Platt, Jonathan M; Keyes, Katherine M; Galea, Sandro

2017-12-01

Maximizing both efficiency and equity are core considerations for population health. These considerations can result in tension in population health science as we seek to improve overall population health while achieving equitable health distributions within populations. Limited work has explored empirically the consequences of different population health intervention strategies on the burden of disease and on within- and between-group differences in disease. To address this gap, we compared the impact of four simulated interventions using data from the National Health and Nutrition Examination Survey. In particular, we focus on assessing how population and high-risk primary prevention and population and high-risk secondary interventions efforts to reduce smoking behavior influence systolic blood pressure (SBP) and hypertension, and how such strategies influence inequalities in SBP by income. The greatest reductions in SBP mean and standard deviation resulted from the population secondary prevention. High-risk primary and secondary prevention and population secondary prevention programs all yielded substantial reductions in hypertension prevalence. The effect of population primary prevention did little to decrease population SBP mean and standard deviation, as well as hypertension prevalence. Both high-risk strategies had a larger impact in the low-income population, leading to the greatest narrowing the income-related gap in disease. The population prevention strategies had a larger impact in the high-income population. Population health approaches must consider the potential impact on both the whole population and also on those with different levels of risk for disease within a population, including those in under-represented or under-served groups.

Using demographic characteristics of populations to detect spatial fragmentation following suspected ebola outbreaks in great apes.

PubMed

Genton, Céline; Cristescu, Romane; Gatti, Sylvain; Levréro, Florence; Bigot, Elodie; Motsch, Peggy; Le Gouar, Pascaline; Pierre, Jean-Sébastien; Ménard, Nelly

2017-09-01

Demographic crashes due to emerging diseases can contribute to population fragmentation and increase extinction risk of small populations. Ebola outbreaks in 2002-2004 are suspected to have caused a decline of more than 80% in some Western lowland gorilla (Gorilla gorilla gorilla) populations. We investigated whether demographic indicators of this event allowed for the detection of spatial fragmentation in gorilla populations. We collected demographic data from two neighbouring populations: the Lokoué population, suspected to have been affected by an Ebola outbreak (followed from 2001 to 2014), and the Romani population, of unknown demographic status before Ebola outbreaks (followed from 2005 to 2014). Ten years after the outbreak, the Lokoué population is slowly recovering and the short-term demographic indicators of a population crash were no longer detectable. The Lokoué population has not experienced any additional demographic perturbation over the past decade. The Romani population did not show any of the demographic indicators of a population crash over the past decade. Its demographic structure remained similar to that of unaffected populations. Our results highlighted that the Ebola disease could contribute to fragmentation of gorilla populations due to the spatially heterogeneous impact of its outbreaks. The demographic structure of populations (i.e., age-sex and group structure) can be useful indicators of a possible occurrence of recent Ebola outbreaks in populations without known history, and may be more broadly used in other emerging disease/species systems. Longitudinal data are critical to our understanding of the impact of emerging diseases on wild populations and their conservation. © 2017 Wiley Periodicals, Inc.

Indigenous and tribal peoples' health (The Lancet-Lowitja Institute Global Collaboration): a population study.

PubMed

Anderson, Ian; Robson, Bridget; Connolly, Michele; Al-Yaman, Fadwa; Bjertness, Espen; King, Alexandra; Tynan, Michael; Madden, Richard; Bang, Abhay; Coimbra, Carlos E A; Pesantes, Maria Amalia; Amigo, Hugo; Andronov, Sergei; Armien, Blas; Obando, Daniel Ayala; Axelsson, Per; Bhatti, Zaid Shakoor; Bhutta, Zulfiqar Ahmed; Bjerregaard, Peter; Bjertness, Marius B; Briceno-Leon, Roberto; Broderstad, Ann Ragnhild; Bustos, Patricia; Chongsuvivatwong, Virasakdi; Chu, Jiayou; Deji; Gouda, Jitendra; Harikumar, Rachakulla; Htay, Thein Thein; Htet, Aung Soe; Izugbara, Chimaraoke; Kamaka, Martina; King, Malcolm; Kodavanti, Mallikharjuna Rao; Lara, Macarena; Laxmaiah, Avula; Lema, Claudia; Taborda, Ana María León; Liabsuetrakul, Tippawan; Lobanov, Andrey; Melhus, Marita; Meshram, Indrapal; Miranda, J Jaime; Mu, Thet Thet; Nagalla, Balkrishna; Nimmathota, Arlappa; Popov, Andrey Ivanovich; Poveda, Ana María Peñuela; Ram, Faujdar; Reich, Hannah; Santos, Ricardo V; Sein, Aye Aye; Shekhar, Chander; Sherpa, Lhamo Y; Skold, Peter; Tano, Sofia; Tanywe, Asahngwa; Ugwu, Chidi; Ugwu, Fabian; Vapattanawong, Patama; Wan, Xia; Welch, James R; Yang, Gonghuan; Yang, Zhaoqing; Yap, Leslie

2016-07-09

International studies of the health of Indigenous and tribal peoples provide important public health insights. Reliable data are required for the development of policy and health services. Previous studies document poorer outcomes for Indigenous peoples compared with benchmark populations, but have been restricted in their coverage of countries or the range of health indicators. Our objective is to describe the health and social status of Indigenous and tribal peoples relative to benchmark populations from a sample of countries. Collaborators with expertise in Indigenous health data systems were identified for each country. Data were obtained for population, life expectancy at birth, infant mortality, low and high birthweight, maternal mortality, nutritional status, educational attainment, and economic status. Data sources consisted of governmental data, data from non-governmental organisations such as UNICEF, and other research. Absolute and relative differences were calculated. Our data (23 countries, 28 populations) provide evidence of poorer health and social outcomes for Indigenous peoples than for non-Indigenous populations. However, this is not uniformly the case, and the size of the rate difference varies. We document poorer outcomes for Indigenous populations for: life expectancy at birth for 16 of 18 populations with a difference greater than 1 year in 15 populations; infant mortality rate for 18 of 19 populations with a rate difference greater than one per 1000 livebirths in 16 populations; maternal mortality in ten populations; low birthweight with the rate difference greater than 2% in three populations; high birthweight with the rate difference greater than 2% in one population; child malnutrition for ten of 16 populations with a difference greater than 10% in five populations; child obesity for eight of 12 populations with a difference greater than 5% in four populations; adult obesity for seven of 13 populations with a difference greater than 10% in four populations; educational attainment for 26 of 27 populations with a difference greater than 1% in 24 populations; and economic status for 15 of 18 populations with a difference greater than 1% in 14 populations. We systematically collated data across a broader sample of countries and indicators than done in previous studies. Taking into account the UN Sustainable Development Goals, we recommend that national governments develop targeted policy responses to Indigenous health, improving access to health services, and Indigenous data within national surveillance systems. The Lowitja Institute. Copyright © 2016 Elsevier Ltd. All rights reserved.

Extinction-effective population index: incorporating life-history variations in population viability analysis.

PubMed

Fujiwara, Masami

2007-09-01

Viability status of populations is a commonly used measure for decision-making in the management of populations. One of the challenges faced by managers is the need to consistently allocate management effort among populations. This allocation should in part be based on comparison of extinction risks among populations. Unfortunately, common criteria that use minimum viable population size or count-based population viability analysis (PVA) often do not provide results that are comparable among populations, primarily because they lack consistency in determining population size measures and threshold levels of population size (e.g., minimum viable population size and quasi-extinction threshold). Here I introduce a new index called the "extinction-effective population index," which accounts for differential effects of demographic stochasticity among organisms with different life-history strategies and among individuals in different life stages. This index is expected to become a new way of determining minimum viable population size criteria and also complement the count-based PVA. The index accounts for the difference in life-history strategies of organisms, which are modeled using matrix population models. The extinction-effective population index, sensitivity, and elasticity are demonstrated in three species of Pacific salmonids. The interpretation of the index is also provided by comparing them with existing demographic indices. Finally, a measure of life-history-specific effect of demographic stochasticity is derived.

A framework for estimating the determinants of spatial and temporal variation in vital rates and inferring the occurrence of unobserved extreme events

PubMed Central

Jesenšek, Dušan; Crivelli, Alain J.

2018-01-01

We develop a general framework that combines long-term tag–recapture data and powerful statistical and modelling techniques to investigate how population, environmental and climate factors determine variation in vital rates and population dynamics in an animal species, using as a case study the population of brown trout living in Upper Volaja (Western Slovenia). This population has been monitored since 2004. Upper Volaja is a sink, receiving individuals from a source population living above a waterfall. We estimate the numerical contribution of the source population on the sink population and test the effects of temperature, population density and extreme events on variation in vital rates among 2647 individually tagged brown trout. We found that individuals dispersing downstream from the source population help maintain high population densities in the sink population despite poor recruitment. The best model of survival for individuals older than juveniles includes additive effects of birth cohort and sampling occasion. Fast growth of older cohorts and higher population densities in 2004–2005 suggest very low population densities in the late 1990s, which we hypothesize were caused by a flash flood that strongly reduced population size and created the habitat conditions for faster individual growth and transient higher population densities after the extreme event. PMID:29657746

Inferring ancient Agave cultivation practices from contemporary genetic patterns.

PubMed

Parker, Kathleen C; Trapnell, Dorset W; Hamrick, J L; Hodgson, Wendy C; Parker, Albert J

2010-04-01

Several Agave species have played an important ethnobotanical role since prehistory in Mesoamerica and semiarid areas to the north, including central Arizona. We examined genetic variation in relict Agave parryi populations northeast of the Mogollon Rim in Arizona, remnants from anthropogenic manipulation over 600 years ago. We used both allozymes and microsatellites to compare genetic variability and structure in anthropogenically manipulated populations with putative wild populations, to assess whether they were actively cultivated or the result of inadvertent manipulation, and to determine probable source locations for anthropogenic populations. Wild populations were more genetically diverse than anthropogenic populations, with greater expected heterozygosity, polymorphic loci, effective number of alleles and allelic richness. Anthropogenic populations exhibited many traits indicative of past active cultivation: fixed heterozygosity for several loci in all populations (nonexistent in wild populations); fewer multilocus genotypes, which differed by fewer alleles; and greater differentiation among populations than was characteristic of wild populations. Furthermore, manipulated populations date from a period when changes in the cultural context may have favoured active cultivation near dwellings. Patterns of genetic similarity among populations suggest a complex anthropogenic history. Anthropogenic populations were not simply derived from the closest wild A. parryi stock; instead they evidently came from more distant, often more diverse, wild populations, perhaps obtained through trade networks in existence at the time of cultivation.

[Genetic differentiation of Isaria farinosa populations in Anhui Province of East China].

PubMed

Sun, Zhao-Hong; Luan, Feng-Gang; Zhang, Da-Min; Chen, Ming-Jun; Wang, Bin; Li, Zeng-Zhi

2011-11-01

Isaria farinosa is an important entomopathogenic fungus. By using ISSR, this paper studied the genetic heterogeneity of six I. farinosa populations at different localities of Anhui Province, East China. A total of 98.5% polymorphic loci were amplified with ten polymorphic primers, but the polymorphism at population level varied greatly, within the range of 59.6%-93.2%. The genetic differentiation index (G(st)) between the populations based on Nei's genetic heterogenesis analysis was 0.3365, and the gene flow (N(m)) was 0.4931. The genetic differentiation between the populations was lower than that within the populations, suggesting that the genetic variation of I. farinosa mainly come from the interior of the populations. The UPGMA clustering based on the genetic similarities between the isolates revealed that the Xishan population was monophylectic, while the other five populations were polyphylectic, with the Yaoluoping population being the most heterogenic and the Langyashan population being the least heterogenic. No correlations were observed between the geographic distance and the genetic distance of the populations. According to the UPGMA clustering based on the genetic distance between the populations, the six populations were classified into three groups, and this classification was accorded with the clustering based on geographic environment, suggesting the effects of environmental heterogeneity on the population heterogeneity.

A framework for estimating the determinants of spatial and temporal variation in vital rates and inferring the occurrence of unobserved extreme events.

PubMed

Vincenzi, Simone; Jesenšek, Dušan; Crivelli, Alain J

2018-03-01

We develop a general framework that combines long-term tag-recapture data and powerful statistical and modelling techniques to investigate how population, environmental and climate factors determine variation in vital rates and population dynamics in an animal species, using as a case study the population of brown trout living in Upper Volaja (Western Slovenia). This population has been monitored since 2004. Upper Volaja is a sink, receiving individuals from a source population living above a waterfall. We estimate the numerical contribution of the source population on the sink population and test the effects of temperature, population density and extreme events on variation in vital rates among 2647 individually tagged brown trout. We found that individuals dispersing downstream from the source population help maintain high population densities in the sink population despite poor recruitment. The best model of survival for individuals older than juveniles includes additive effects of birth cohort and sampling occasion. Fast growth of older cohorts and higher population densities in 2004-2005 suggest very low population densities in the late 1990s, which we hypothesize were caused by a flash flood that strongly reduced population size and created the habitat conditions for faster individual growth and transient higher population densities after the extreme event.

Genetic variation and co-variation for fitness between intra-population and inter-population backgrounds in the red flour beetle, Tribolium castaneum

PubMed Central

Drury, Douglas W.; Wade, Michael J.

2010-01-01

Hybrids from crosses between populations of the flour beetle, Tribolium castaneum, express varying degrees of inviability and morphological abnormalities. The proportion of allopatric population hybrids exhibiting these negative hybrid phenotypes varies widely, from 3% to 100%, depending upon the pair of populations crossed. We crossed three populations and measured two fitness components, fertility and adult offspring numbers from successful crosses, to determine how genes segregating within populations interact in inter-population hybrids to cause the negative phenotypes. With data from crosses of 40 sires from each of three populations to groups of 5 dams from their own and two divergent populations, we estimated the genetic variance and covariance for breeding value of fitness between the intra- and inter-population backgrounds and the sire × dam-population interaction variance. The latter component of the variance in breeding values estimates the change in genic effects between backgrounds owing to epistasis. Interacting genes with a positive effect, prior to fixation, in the sympatric background but a negative effect in the hybrid background cause reproductive incompatibility in the Dobzhansky-Muller speciation model. Thus, the sire × dam-population interaction provides a way to measure the progress toward speciation of genetically differentiating populations on a trait by trait basis using inter-population hybrids. PMID:21044199

Genetic composition of captive panda population.

PubMed

Yang, Jiandong; Shen, Fujun; Hou, Rong; Da, Yang

2016-10-03

A major function of the captive panda population is to preserve the genetic diversity of wild panda populations in their natural habitats. Understanding the genetic composition of the captive panda population in terms of genetic contributions from the wild panda populations provides necessary knowledge for breeding plans to preserve the genetic diversity of the wild panda populations. The genetic contributions from different wild populations to the captive panda population were highly unbalanced, with Qionglai accounting for 52.2 % of the captive panda gene pool, followed by Minshan with 21.5 %, Qinling with 10.6 %, Liangshan with 8.2 %, and Xiaoxiangling with 3.6 %, whereas Daxiangling, which had similar population size as Xiaoxiangling, had no genetic representation in the captive population. The current breeding recommendations may increase the contribution of some small wild populations at the expense of decreasing the contributions of other small wild populations, i.e., increasing the Xiaoxiangling contribution while decreasing the contribution of Liangshan, or sharply increasing the Qinling contribution while decreasing the contributions of Xiaoxiangling and Liangshan, which were two of the three smallest wild populations and were already severely under-represented in the captive population. We developed three habitat-controlled breeding plans that could increase the genetic contributions from the smallest wild populations to 6.7-11.2 % for Xiaoxiangling, 11.5-12.3 % for Liangshan and 12.9-20.0 % for Qinling among the offspring of one breeding season while reducing the risk of hidden inbreeding due to related founders from the same habitat undetectable by pedigree data. The three smallest wild panda populations of Daxiangling, Xiaoxiangling and Liangshan either had no representation or were severely unrepresented in the current captive panda population. By incorporating the breeding goal of increasing the genetic contributions from the smallest wild populations into breeding plans, the severely under-represented small wild populations in the current captive panda population could be increased steadily for the near future.

Colonial, more widely distributed and less abundant bird species undergo wider population fluctuations independent of their population trend

PubMed Central

Møller, Anders P.

2017-01-01

Understanding temporal variability in population size is important for conservation biology because wide population fluctuations increase the risk of extinction. Previous studies suggested that certain ecological, demographic, life-history and genetic characteristics of species might be related to the degree of their population fluctuations. We checked whether that was the case in a large sample of 231 European breeding bird species while taking a number of potentially confounding factors such as population trends or similarities among species due to common descent into account. When species-specific characteristics were analysed one by one, the magnitude of population fluctuations was positively related to coloniality, habitat, total breeding range, heterogeneity of breeding distribution and natal dispersal, and negatively related to urbanisation, abundance, relative number of subspecies, parasitism and proportion of polymorphic loci. However, when abundance (population size) was included in the analyses of the other parameters, only coloniality, habitat, total breeding range and abundance remained significantly related to population fluctuations. The analysis including all these predictors simultaneously showed that population size fluctuated more in colonial, less abundant species with larger breeding ranges. Other parameters seemed to be related to population fluctuations only because of their association with abundance or coloniality. The unexpected positive relationship between population fluctuations and total breeding range did not seem to be mediated by abundance. The link between population fluctuations and coloniality suggests a previously unrecognized cost of coloniality. The negative relationship between population size and population fluctuations might be explained by at least three types of non-mutually exclusive stochastic processes: demographic, environmental and genetic stochasticity. Measurement error in population indices, which was unknown, may have contributed to the negative relationship between population size and fluctuations, but apparently only to a minor extent. The association between population size and fluctuations suggests that populations might be stabilized by increasing population size. PMID:28253345

Farm Population of the United States: 1974. Current Population Reports, Farm Population.

ERIC Educational Resources Information Center

Banks, Vera J.; And Others

Based on data derived primarily from the Current Population Survey of the Bureau of the Census, this statistical report presents demographic and labor force characteristics of the U.S. farm population and a comparison of selected characteristics of the farm and nonfarm population. Tabular data are presented as follows: (1) Population of the U.S.,…

Farm Population of the United States: 1971. Current Population Reports: Farm Population.

ERIC Educational Resources Information Center

Bureau of the Census (DOC), Suitland, MD. Population Div.

Based on data derived from the Current Population Survey of the Bureau of the Census, this statistical report presents demographic and labor force characteristics of the U.S. farm population and comparisons of the farm and nonfarm populations. Tabular data are presented as follows: (1) U.S. Population, Total and Farm: April 1960 and 1971; (2)…

Farm Population of the United States: 1972. Current Population Reports: Farm Population.

ERIC Educational Resources Information Center

Bureau of the Census (DOC), Suitland, MD. Population Div.

Based on data derived from the Current Population Survey of the Bureau of Census, this statistical report presents demographic and labor force characteristics of the U.S. farm population and comparisons of the farm and nonfarm populations. Tabular data are presented as follows: (1) U.S. Population, Total and Farm: April 1960 to 1972; (2) Persons…

Consequences of the Allee effect and intraspecific competition on population persistence under adverse environmental conditions.

PubMed

Petrovskii, Sergei; Blackshaw, Rod; Li, Bai-Lian

2008-02-01

The impact of intraspecific interactions on ecological stability and population persistence in terms of steady state(s) existence is considered theoretically based on a general competition model. We compare persistence of a structured population consisting of a few interacting (competitive) subpopulations, or groups, to persistence of the corresponding unstructured population. For a general case, we show that if the intra-group competition is stronger than the inter-group competition, then the structured population is less prone to extinction, i.e. it can persist in a parameter range where the unstructured population goes extinct. For a more specific case of a population with hierarchical competition, we show that relative viability of structured and unstructured populations depend on the type of density dependence in the population growth. Namely, while in the case of logistic growth, structured and unstructured populations exhibit equivalent persistence; in the case of Allee dynamics, the persistence of a hierarchically structured population is shown to be higher. We then apply these results to the case of behaviourally structured populations and demonstrate that an extreme form of individual aggression can be beneficial at the population level and enhance population persistence.

SOCIODEMOGRAPHIC DATA USED FOR IDENTIFYING ...

EPA Pesticide Factsheets

Due to unique social and demographic characteristics, various segments of the population may experience exposures different from those of the general population, which, in many cases, may be greater. When risk assessments do not characterize subsets of the general population, the populations that may experience the greatest risk remain unidentified. When such populations are not identified, the social and demographic data relevant to these populations is not considered when preparing exposure estimates, which can underestimate exposure and risk estimates for at-risk populations. Thus, it is necessary for risk or exposure assessors characterizing a diverse population, to first identify and then enumerate certain groups within the general population who are at risk for greater contaminant exposures. The document entitled Sociodemographic Data Used for Identifying Potentially Highly Exposed Populations (also referred to as the Highly Exposed Populations document), assists assessors in identifying and enumerating potentially highly exposed populations. This document presents data relating to factors which potentially impact an individual or group's exposure to environmental contaminants based on activity patterns (how time is spent), microenvironments (locations where time is spent), and other socio-demographic data such as age, gender, race and economic status. Populations potentially more exposed to various chemicals of concern, relative to the general population

Effective population size of korean populations.

PubMed

Park, Leeyoung

2014-12-01

Recently, new methods have been developed for estimating the current and recent changes in effective population sizes. Based on the methods, the effective population sizes of Korean populations were estimated using data from the Korean Association Resource (KARE) project. The overall changes in the population sizes of the total populations were similar to CHB (Han Chinese in Beijing, China) and JPT (Japanese in Tokyo, Japan) of the HapMap project. There were no differences in past changes in population sizes with a comparison between an urban area and a rural area. Age-dependent current and recent effective population sizes represent the modern history of Korean populations, including the effects of World War II, the Korean War, and urbanization. The oldest age group showed that the population growth of Koreans had already been substantial at least since the end of the 19th century.

Fundamental population-productivity relationships can be modified through density-dependent feedbacks of life-history evolution.

PubMed

Kuparinen, Anna; Stenseth, Nils Christian; Hutchings, Jeffrey A

2014-12-01

The evolution of life histories over contemporary time scales will almost certainly affect population demography. One important pathway for such eco-evolutionary interactions is the density-dependent regulation of population dynamics. Here, we investigate how fisheries-induced evolution (FIE) might alter density-dependent population-productivity relationships. To this end, we simulate the eco-evolutionary dynamics of an Atlantic cod (Gadus morhua) population under fishing, followed by a period of recovery in the absence of fishing. FIE is associated with increases in juvenile production, the ratio of juveniles to mature population biomass, and the ratio of the mature population biomass relative to the total population biomass. In contrast, net reproductive rate (R 0 ) and per capita population growth rate (r) decline concomitantly with evolution. Our findings suggest that FIE can substantially modify the fundamental population-productivity relationships that underlie density-dependent population regulation and that form the primary population-dynamical basis for fisheries stock-assessment projections. From a conservation and fisheries-rebuilding perspective, we find that FIE reduces R 0 and r, the two fundamental correlates of population recovery ability and inversely extinction probability.

Strong population structure of Schizopygopsis chengi and the origin of S. chengi baoxingensis revealed by mtDNA and microsatellite markers.

PubMed

Liu, Dongqi; Hou, Feixia; Liu, Qin; Zhang, Xiuyue; Yan, Taiming; Song, Zhaobin

2015-02-01

The Tibetan Plateau underwent dramatic geological and climatic changes, which had important implications for genetic divergence and population dynamics of freshwater fish populations. Fluctuations of the ecogeographical environment and major hydrographic formations might have promoted the formation of new subspecies or species. In order to understand the impact of plateau uplift on freshwater fish evolutionary history, we estimated the genetic diversity and population structure in two subspecies of Schizopygopsis chengi (S. c. chengi and S. c. baoxingensis) in upper Yangtze River in Tibetan Plateau area using mitochondrial DNA control region and eight microsatellite markers, which suggested that there was a close genetic relationship. S. chengi showed some significant genetic structure that did not correlate with geographic distance. Bayesian assignment tests indicated that S. chengi samples in the study could be divided into four populations: upstream population, midstream population, tributary population and S. c. baoxingensis population. S. c. chengi and S. c. baoxingensis showed significant genetic divergence. However, phylogenetic analysis, population structure analysis and historical gene flow estimation suggested that there was close genetic relationship between S. c. baoxingensis and the Dawei population which belongs to populations of S. c. chengi. The time that Dawei population suffered from a bottleneck and S. c. baoxingensis underwent population expansion was congruent with the last glacial period on the Tibetan Plateau. The results confirmed the hypothesis that the Dawei River and Baoxing River were once connected, and the Dawei and Baoxing populations originated from a single population, but were isolated into separate populations because of crustal movements and the Baoxing population evolved as S. c. baoxingensis.

Population genetic diversity and structure of a naturally isolated plant species, Rhodiola dumulosa (Crassulaceae).

PubMed

Hou, Yan; Lou, Anru

2011-01-01

Rhodiola dumulosa (Crassulaceae) is a perennial diploid species found in high-montane areas. It is distributed in fragmented populations across northern, central and northwestern China. In this study, we aimed to (i) measure the genetic diversity of this species and that of its populations; (ii) describe the genetic structure of these populations across the entire distribution range in China; and (iii) evaluate the extent of gene flow among the naturally fragmented populations. Samples from 1089 individuals within 35 populations of R. dumulosa were collected, covering as much of the entire distribution range of this species within China as possible. Population genetic diversity and structure were analyzed using AFLP molecular markers. Gene flow among populations was estimated according to the level of population differentiation. The total genetic diversity of R. dumulosa was high but decreased with increasing altitude. Population-structure analysis indicated that the most closely related populations were geographically restricted and occurred in close proximity to each other. A significant isolation-by-distance pattern, caused by the naturally fragmented population distribution, was observed. At least two distinct gene pools were found in the 35 sampled populations, one composed of populations in northern China and the other composed of populations in central and northwestern China. The calculation of Nei's gene diversity index revealed that the genetic diversity in the northern China pool (0.1972) was lower than that in the central and northwestern China pool (0.2216). The populations were significantly isolated, and gene flow was restricted throughout the entire distribution. However, gene flow among populations on the same mountain appears to be unrestricted, as indicated by the weak genetic isolation among these populations.

Population Genetic Diversity and Structure of a Naturally Isolated Plant Species, Rhodiola dumulosa (Crassulaceae)

PubMed Central

Hou, Yan; Lou, Anru

2011-01-01

Aims Rhodiola dumulosa (Crassulaceae) is a perennial diploid species found in high-montane areas. It is distributed in fragmented populations across northern, central and northwestern China. In this study, we aimed to (i) measure the genetic diversity of this species and that of its populations; (ii) describe the genetic structure of these populations across the entire distribution range in China; and (iii) evaluate the extent of gene flow among the naturally fragmented populations. Methods Samples from 1089 individuals within 35 populations of R. dumulosa were collected, covering as much of the entire distribution range of this species within China as possible. Population genetic diversity and structure were analyzed using AFLP molecular markers. Gene flow among populations was estimated according to the level of population differentiation. Important Findings The total genetic diversity of R. dumulosa was high but decreased with increasing altitude. Population-structure analysis indicated that the most closely related populations were geographically restricted and occurred in close proximity to each other. A significant isolation-by-distance pattern, caused by the naturally fragmented population distribution, was observed. At least two distinct gene pools were found in the 35 sampled populations, one composed of populations in northern China and the other composed of populations in central and northwestern China. The calculation of Nei's gene diversity index revealed that the genetic diversity in the northern China pool (0.1972) was lower than that in the central and northwestern China pool (0.2216). The populations were significantly isolated, and gene flow was restricted throughout the entire distribution. However, gene flow among populations on the same mountain appears to be unrestricted, as indicated by the weak genetic isolation among these populations. PMID:21909437

Pathological Differences in Heterodera schachtii Populations

PubMed Central

Griffin, G. D.

1981-01-01

Five populations of Heterodera schachtii Schm. from Oregon, Idaho, and Utah did not differ significantly in seedling penetration and rate of emergence and virulence. Another Utah H. schachtii population (Utah 2), however, differed from these five populations in all of the above-mentioned characteristics. More H. schachtii larvae of the Utah 2 population than the other populations penetrated sugarbeet seedlings at 10, 15, 20, and 25 C. Root and top weights of sugarbeet plants were signiticantly less when roots were parasitized by the Utah 2 population than when they were parasitized by larvae of the other nematode populations under similar experimental conditions. Also, the period of larval emergence was shorter in the Utah 2 population than in any of the other H. schachtii populations. PMID:19300743

Genomic Consequences of Population Decline in the Endangered Florida Scrub-Jay.

PubMed

Chen, Nancy; Cosgrove, Elissa J; Bowman, Reed; Fitzpatrick, John W; Clark, Andrew G

2016-11-07

Understanding the population genetic consequences of declining population size is important for conserving the many species worldwide facing severe decline [1]. Thorough empirical studies on the impacts of population reduction at a genome-wide scale in the wild are scarce because they demand huge field and laboratory investments [1, 2]. Previous studies have demonstrated the importance of gene flow in introducing genetic variation to small populations [3], but few have documented both genetic and fitness consequences of decreased immigration through time in a natural population [4-6]. Here we assess temporal variation in gene flow, inbreeding, and fitness using longitudinal genomic, demographic, and phenotypic data from a long-studied population of federally Threatened Florida scrub-jays (Aphelocoma coerulescens). We exhaustively sampled and genotyped the study population over two decades, providing one of the most detailed longitudinal investigations of genetics in a wild animal population to date. Immigrants were less heterozygous than residents but still introduced genetic variation into our study population. Owing to regional population declines, immigration into the study population declined from 1995-2013, resulting in increased levels of inbreeding and reduced fitness via inbreeding depression, even as the population remained demographically stable. Our results show that, contrary to conventional wisdom, small peripheral populations that already have undergone a genetic bottleneck may play a vital role in preserving genetic diversity of larger and seemingly stable populations. These findings underscore the importance of investing in the persistence of small populations and maintaining population connectivity in conservation of fragmented species. Copyright © 2016 Elsevier Ltd. All rights reserved.

Conservation genetics of evolutionary lineages of the endangered mountain yellow-legged frog, Rana muscosa (Amphibia: Ranidae), in southern California

USGS Publications Warehouse

Schoville, Sean D.; Tustall, Tate S.; Vredenburg, Vance T.; Backlin, Adam R.; Gallegos, Elizabeth; Wood, Dustin A.; Fisher, Robert N.

2011-01-01

Severe population declines led to the listing of southern California Rana muscosa (Ranidae) as endangered in 2002. Nine small populations inhabit watersheds in three isolated mountain ranges, the San Gabriel, San Bernardino and San Jacinto. One population from the Dark Canyon tributary in the San Jacinto Mountains has been used to establish a captive breeding population at the San Diego Zoo Institute for Conservation Research. Because these populations may still be declining, it is critical to gather information on how genetic variation is structured in these populations and what historical inter-population connectivity existed between populations. Additionally, it is not clear whether these populations are rapidly losing genetic diversity due to population bottlenecks. Using mitochondrial and microsatellite data, we examine patterns of genetic variation in southern California and one of the last remaining populations of R. muscosa in the southern Sierra Nevada. We find low levels of genetic variation within each population and evidence of genetic bottlenecks. Additionally, substantial population structure is evident, suggesting a high degree of historical isolation within and between mountain ranges. Based on estimates from a multi-population isolation with migration analysis, these populations diversified during glacial episodes of the Pleistocene, with little gene flow during population divergence. Our data demonstrate that unique evolutionary lineages of R. muscosa occupy each mountain range in southern California and should be managed separately. The captive breeding program at Dark Canyon is promising, although mitigating the loss of neutral genetic diversity relative to the natural population might require additional breeding frogs.

Population Profile of the United States 1984-85.

ERIC Educational Resources Information Center

Current Population Reports, 1987

1987-01-01

This population profile summarizes the wide range of demographic and socio-economic data collected from the Current Population Survey during 1984 and 1985. The report contains information on the following areas: National Population Trends; National Population Projections; Fertility; State Population Trends; The Metropolitan/Nonmetropolitan…

Popullution: A Position Paper on Population.

ERIC Educational Resources Information Center

Durner, Mary Beth

This position paper presents an interdisciplinary approach to the study of population. Six main sections are included in the paper: Introduction, The Growth of the Human Population, The Psychological Effects of Population Growth, Overpopulated America, Myths Concerning Population Growth and Control, and Population Education. Section 1, an…

Realized population change for long-term monitoring: California spotted owl case study

Treesearch

Mary M. Conner; John J. Keane; Claire V. Gallagher; Gretchen Jehle; Thomas E. Munton; Paula A. Shaklee; Ross A. Gerrard

2013-01-01

The annual rate of population change (λt) is a good metric for evaluating population performance because it summarizes survival and recruitment rates and can be used for open populations. Another measure of population performance, realized population change (Δt...

Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations.

PubMed

Kopelman, Naama M; Stone, Lewi; Wang, Chaolong; Gefel, Dov; Feldman, Marcus W; Hillel, Jossi; Rosenberg, Noah A

2009-12-08

Genetic studies have often produced conflicting results on the question of whether distant Jewish populations in different geographic locations share greater genetic similarity to each other or instead, to nearby non-Jewish populations. We perform a genome-wide population-genetic study of Jewish populations, analyzing 678 autosomal microsatellite loci in 78 individuals from four Jewish groups together with similar data on 321 individuals from 12 non-Jewish Middle Eastern and European populations. We find that the Jewish populations show a high level of genetic similarity to each other, clustering together in several types of analysis of population structure. Further, Bayesian clustering, neighbor-joining trees, and multidimensional scaling place the Jewish populations as intermediate between the non-Jewish Middle Eastern and European populations. These results support the view that the Jewish populations largely share a common Middle Eastern ancestry and that over their history they have undergone varying degrees of admixture with non-Jewish populations of European descent.

Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations

PubMed Central

2009-01-01

Background Genetic studies have often produced conflicting results on the question of whether distant Jewish populations in different geographic locations share greater genetic similarity to each other or instead, to nearby non-Jewish populations. We perform a genome-wide population-genetic study of Jewish populations, analyzing 678 autosomal microsatellite loci in 78 individuals from four Jewish groups together with similar data on 321 individuals from 12 non-Jewish Middle Eastern and European populations. Results We find that the Jewish populations show a high level of genetic similarity to each other, clustering together in several types of analysis of population structure. Further, Bayesian clustering, neighbor-joining trees, and multidimensional scaling place the Jewish populations as intermediate between the non-Jewish Middle Eastern and European populations. Conclusion These results support the view that the Jewish populations largely share a common Middle Eastern ancestry and that over their history they have undergone varying degrees of admixture with non-Jewish populations of European descent. PMID:19995433

Genetic diversity affects the strength of population regulation in a marine fish.

PubMed

Johnson, D W; Freiwald, J; Bernardi, G

2016-03-01

Variation is an essential feature of biological populations, yet much of ecological theory treats individuals as though they are identical. This simplifying assumption is often justified by the perception that variation among individuals does not have significant effects on the dynamics of whole populations. However, this perception may be skewed by a historic focus on studying single populations. A true evaluation of the extent to which among-individual variation affects the dynamics of populations requires the study of multiple populations. In this study, we examined variation in the dynamics of populations of a live-bearing, marine fish (black surfperch; Embiotoca jacksoni). In collaboration with an organization of citizen scientists (Reef Check California), we were able to examine the dynamics of eight populations that were distributed throughout approximately 700 km of coastline, a distance that encompasses much of this species' range. We hypothesized that genetic variation within a local population would be related to the intensity of competition and to the strength of population regulation. To test this hypothesis, we examined whether genetic diversity (measured by the diversity of mitochondrial DNA haplotypes) was related to the strength of population regulation. Low-diversity populations experienced strong density dependence in population growth rates and population sizes were regulated much more tightly than they were in high-diversity populations. Mechanisms that contributed to this pattern include links between genetic diversity, habitat use, and spatial crowding. On average, low-diversity populations used less of the available habitat and exhibited greater spatial clustering (and more intense competition) for a given level of density (measured at the scale of the reef). Although the populations we studied also varied with respect to exogenous characteristics (habitat complexity, densities of predators, and interspecific competitors), none of these characteristics was significantly related to the strength of population regulation. In contrast, an endogenous characteristic of the population (genetic diversity) explained 77% of the variation in the strength of population regulation (95% CI: 27-94%). Our results suggest that the genetic and phenotypic composition of populations can play a major role in their dynamics.

Population genetic structure of traditional populations in the Peruvian Central Andes and implications for South American population history.

PubMed

Cabana, Graciela S; Lewis, Cecil M; Tito, Raúl Y; Covey, R Alan; Cáceres, Angela M; Cruz, Augusto F De La; Durand, Diana; Housman, Genevieve; Hulsey, Brannon I; Iannacone, Gian Carlo; López, Paul W; Martínez, Rolando; Medina, Ángel; Dávila, Olimpio Ortega; Pinto, Karla Paloma Osorio; Santillán, Susan I Polo; Domínguez, Percy Rojas; Rubel, Meagan; Smith, Heather F; Smith, Silvia E; Massa, Verónica Rubín de Celis; Lizárraga, Beatriz; Stone, Anne C

2014-01-01

Molecular-based characterizations of Andean peoples are traditionally conducted in the service of elucidating continent-level evolutionary processes in South America. Consequently, genetic variation among "western" Andean populations is often represented in relation to variation among "eastern" Amazon and Orinoco River Basin populations. This west-east contrast in patterns of population genetic variation is typically attributed to large-scale phenomena, such as dual founder colonization events or differing long-term microevolutionary histories. However, alternative explanations that consider the nature and causes of population genetic diversity within the Andean region remain underexplored. Here we examine population genetic diversity in the Peruvian Central Andes using data from the mtDNA first hypervariable region and Y-chromosome short tandem repeats among 17 newly sampled populations and 15 published samples. Using this geographically comprehensive data set, we first reassessed the currently accepted pattern of western versus eastern population genetic structure, which our results ultimately reject: mtDNA population diversities were lower, rather than higher, within Andean versus eastern populations, and only highland Y-chromosomes exhibited significantly higher within-population diversities compared with eastern groups. Multiple populations, including several highland samples, exhibited low genetic diversities for both genetic systems. Second, we explored whether the implementation of Inca state and Spanish colonial policies starting at about ad 1400 could have substantially restructured population genetic variation and consequently constitute a primary explanation for the extant pattern of population diversity in the Peruvian Central Andes. Our results suggest that Peruvian Central Andean population structure cannot be parsimoniously explained as the sole outcome of combined Inca and Spanish policies on the region's population demography: highland populations differed from coastal and lowland populations in mtDNA genetic structure only; highland groups also showed strong evidence of female-biased gene flow and/or effective sizes relative to other Peruvian ecozones. Taken together, these findings indicate that population genetic structure in the Peruvian Central Andes is considerably more complex than previously reported and that characterizations of and explanations for genetic variation may be best pursued within more localized regions and defined time periods.

Estimating finite-population reproductive numbers in heterogeneous populations.

PubMed

Keegan, Lindsay T; Dushoff, Jonathan

2016-05-21

The basic reproductive number, R0, is one of the most important epidemiological quantities. R0 provides a threshold for elimination and determines when a disease can spread or when a disease will die out. Classically, R0 is calculated assuming an infinite population of identical hosts. Previous work has shown that heterogeneity in the host mixing rate increases R0 in an infinite population. However, it has been suggested that in a finite population, heterogeneity in the mixing rate may actually decrease the finite-population reproductive numbers. Here, we outline a framework for discussing different types of heterogeneity in disease parameters, and how these affect disease spread and control. We calculate "finite-population reproductive numbers" with different types of heterogeneity, and show that in a finite population, heterogeneity has complicated effects on the reproductive number. We find that simple heterogeneity decreases the finite-population reproductive number, whereas heterogeneity in the intrinsic mixing rate (which affects both infectiousness and susceptibility) increases the finite-population reproductive number when R0 is small relative to the size of the population and decreases the finite-population reproductive number when R0 is large relative to the size of the population. Although heterogeneity has complicated effects on the finite-population reproductive numbers, its implications for control are straightforward: when R0 is large relative to the size of the population, heterogeneity decreases the finite-population reproductive numbers, making disease control or elimination easier than predicted by R0. Copyright © 2016 Elsevier Ltd. All rights reserved.

Multi-population Genomic Relationships for Estimating Current Genetic Variances Within and Genetic Correlations Between Populations.

PubMed

Wientjes, Yvonne C J; Bijma, Piter; Vandenplas, Jérémie; Calus, Mario P L

2017-10-01

Different methods are available to calculate multi-population genomic relationship matrices. Since those matrices differ in base population, it is anticipated that the method used to calculate genomic relationships affects the estimate of genetic variances, covariances, and correlations. The aim of this article is to define the multi-population genomic relationship matrix to estimate current genetic variances within and genetic correlations between populations. The genomic relationship matrix containing two populations consists of four blocks, one block for population 1, one block for population 2, and two blocks for relationships between the populations. It is known, based on literature, that by using current allele frequencies to calculate genomic relationships within a population, current genetic variances are estimated. In this article, we theoretically derived the properties of the genomic relationship matrix to estimate genetic correlations between populations and validated it using simulations. When the scaling factor of across-population genomic relationships is equal to the product of the square roots of the scaling factors for within-population genomic relationships, the genetic correlation is estimated unbiasedly even though estimated genetic variances do not necessarily refer to the current population. When this property is not met, the correlation based on estimated variances should be multiplied by a correction factor based on the scaling factors. In this study, we present a genomic relationship matrix which directly estimates current genetic variances as well as genetic correlations between populations. Copyright © 2017 by the Genetics Society of America.

Effects of constant immigration on the dynamics and persistence of stable and unstable Drosophila populations

PubMed Central

Dey, Snigdhadip; Joshi, Amitabh

2013-01-01

Constant immigration can stabilize population size fluctuations but its effects on extinction remain unexplored. We show that constant immigration significantly reduced extinction in fruitfly populations with relatively stable or unstable dynamics. In unstable populations with oscillations of amplitude around 1.5 times the mean population size, persistence and constancy were unrelated. Low immigration enhanced persistence without affecting constancy whereas high immigration increased constancy without enhancing persistence. In relatively stable populations with erratic fluctuations of amplitude close to the mean population size, both low and high immigration enhanced persistence. In these populations, the amplitude of fluctuations relative to mean population size went down due to immigration, and their dynamics were altered to low-period cycles. The effects of immigration on the population size distribution and intrinsic dynamics of stable versus unstable populations differed considerably, suggesting that the mechanisms by which immigration reduced extinction risk depended on underlying dynamics in complex ways. PMID:23470546

Making a stand: five centuries of population growth in colonizing populations of Pinus ponderosa.

PubMed

Lesser, Mark R; Jackson, Stephen T

2012-05-01

The processes underlying the development of new populations are important for understanding how species colonize new territory and form viable long-term populations. Life-history-mediated processes such as Allee effects and dispersal capability may interact with climate variability and site-specific factors to govern population success and failure over extended time frames. We studied four disjunct populations of ponderosa pine in the Bighorn Basin of north-central Wyoming to examine population growth spanning more than five centuries. The study populations are separated from continuous ponderosa pine forest by distances ranging from 15 to >100 km. Strong evidence indicates that the initial colonizing individuals are still present, yielding a nearly complete record of population history. All trees in each population were aged using dendroecological techniques. The populations were all founded between 1530 and 1655 cal yr CE. All show logistic growth patterns, with initial exponential growth followed by a slowing during the mid to late 20th century. Initial population growth was slower than expectations from a logistic regression model at all four populations, but increased during the mid-18th century. Initial lags in population growth may have been due to strong Allee effects. A combination of overcoming Allee effects and a transition to favorable climate conditions may have facilitated a mid-18th century pulse in population growth rate.

Type 2 diabetes mellitus: distribution of genetic markers in Kazakh population.

PubMed

Sikhayeva, Nurgul; Talzhanov, Yerkebulan; Iskakova, Aisha; Dzharmukhanov, Jarkyn; Nugmanova, Raushan; Zholdybaeva, Elena; Ramanculov, Erlan

2018-01-01

Ethnic differences exist in the frequencies of genetic variations that contribute to the risk of common disease. This study aimed to analyse the distribution of several genes, previously associated with susceptibility to type 2 diabetes and obesity-related phenotypes, in a Kazakh population. A total of 966 individuals belonging to the Kazakh ethnicity were recruited from an outpatient clinic. We genotyped 41 common single nucleotide polymorphisms (SNPs) previously associated with type 2 diabetes in other ethnic groups and 31 of these were in Hardy-Weinberg equilibrium. The obtained allele frequencies were further compared to publicly available data from other ethnic populations. Allele frequencies for other (compared) populations were pooled from the haplotype map (HapMap) database. Principal component analysis (PCA), cluster analysis, and multidimensional scaling (MDS) were used for the analysis of genetic relationship between the populations. Comparative analysis of allele frequencies of the studied SNPs showed significant differentiation among the studied populations. The Kazakh population was grouped with Asian populations according to the cluster analysis and with the Caucasian populations according to PCA. According to MDS, results of the current study show that the Kazakh population holds an intermediate position between Caucasian and Asian populations. A high percentage of population differentiation was observed between Kazakh and world populations. The Kazakh population was clustered with Caucasian populations, and this result may indicate a significant Caucasian component in the Kazakh gene pool.

Who and what is a "population"? Historical debates, current controversies, and implications for understanding "population health" and rectifying health inequities.

PubMed

Krieger, Nancy

2012-12-01

The idea of "population" is core to the population sciences but is rarely defined except in statistical terms. Yet who and what defines and makes a population has everything to do with whether population means are meaningful or meaningless, with profound implications for work on population health and health inequities. In this article, I review the current conventional definitions of, and historical debates over, the meaning(s) of "population," trace back the contemporary emphasis on populations as statistical rather than substantive entities to Adolphe Quetelet's powerful astronomical metaphor, conceived in the 1830s, of l'homme moyen (the average man), and argue for an alternative definition of populations as relational beings. As informed by the ecosocial theory of disease distribution, I then analyze several case examples to explore the utility of critical population-informed thinking for research, knowledge, and policy involving population health and health inequities. Four propositions emerge: (1) the meaningfulness of means depends on how meaningfully the populations are defined in relation to the inherent intrinsic and extrinsic dynamic generative relationships by which they are constituted; (2) structured chance drives population distributions of health and entails conceptualizing health and disease, including biomarkers, as embodied phenotype and health inequities as historically contingent; (3) persons included in population health research are study participants, and the casual equation of this term with "study population" should be avoided; and (4) the conventional cleavage of "internal validity" and "generalizability" is misleading, since a meaningful choice of study participants must be in relation to the range of exposures experienced (or not) in the real-world societies, that is, meaningful populations, of which they are a part. To improve conceptual clarity, causal inference, and action to promote health equity, population sciences need to expand and deepen their theorizing about who and what makes populations and their means. © 2012 Milbank Memorial Fund.

Population size, center-periphery, and seed dispersers' effects on the genetic diversity and population structure of the Mediterranean relict shrub Cneorum tricoccon.

PubMed

Lázaro-Nogal, Ana; Matesanz, Silvia; García-Fernández, Alfredo; Traveset, Anna; Valladares, Fernando

2017-09-01

The effect of population size on population genetic diversity and structure has rarely been studied jointly with other factors such as the position of a population within the species' distribution range or the presence of mutualistic partners influencing dispersal. Understanding these determining factors for genetic variation is critical for conservation of relict plants that are generally suffering from genetic deterioration. Working with 16 populations of the vulnerable relict shrub Cneorum tricoccon throughout the majority of its western Mediterranean distribution range, and using nine polymorphic microsatellite markers, we examined the effects of periphery (peripheral vs. central), population size (large vs. small), and seed disperser (introduced carnivores vs. endemic lizards) on the genetic diversity and population structure of the species. Contrasting genetic variation ( H E : 0.04-0.476) was found across populations. Peripheral populations showed lower genetic diversity, but this was dependent on population size. Large peripheral populations showed high levels of genetic diversity, whereas small central populations were less diverse. Significant isolation by distance was detected, indicating that the effect of long-distance gene flow is limited relative to that of genetic drift, probably due to high selfing rates ( F IS  = 0.155-0.887), restricted pollen flow, and ineffective seed dispersal. Bayesian clustering also supported the strong population differentiation and highly fragmented structure. Contrary to expectations, the type of disperser showed no significant effect on either population genetic diversity or structure. Our results challenge the idea of an effect of periphery per se that can be mainly explained by population size, drawing attention to the need of integrative approaches considering different determinants of genetic variation. Furthermore, the very low genetic diversity observed in several small populations and the strong among-population differentiation highlight the conservation value of large populations throughout the species' range, particularly in light of climate change and direct human threats.

25 CFR Appendix B to Subpart C - Population Adjustment Factor

Code of Federal Regulations, 2013 CFR

2013-04-01

... the amount available to the first population range. ** The number of tribes changes yearly. *** The..., multiply the Distribution Factor by the total number of tribes identified in the population range to... Population Range 1 . . . 5 = Population Ranges 1 through 5 Nn = Number of tribes in the nth Population Range...

25 CFR Appendix B to Subpart C - Population Adjustment Factor

Code of Federal Regulations, 2014 CFR

2014-04-01

... the amount available to the first population range. ** The number of tribes changes yearly. *** The..., multiply the Distribution Factor by the total number of tribes identified in the population range to... Population Range 1 . . . 5 = Population Ranges 1 through 5 Nn = Number of tribes in the nth Population Range...

25 CFR Appendix B to Subpart C - Population Adjustment Factor

Code of Federal Regulations, 2012 CFR

2012-04-01

... the amount available to the first population range. ** The number of tribes changes yearly. *** The..., multiply the Distribution Factor by the total number of tribes identified in the population range to... Population Range 1 . . . 5 = Population Ranges 1 through 5 Nn = Number of tribes in the nth Population Range...

25 CFR Appendix B to Subpart C - Population Adjustment Factor

Code of Federal Regulations, 2011 CFR

2011-04-01

... the amount available to the first population range. ** The number of tribes changes yearly. *** The..., multiply the Distribution Factor by the total number of tribes identified in the population range to... Population Range 1 . . . 5 = Population Ranges 1 through 5 Nn = Number of tribes in the nth Population Range...

Mapping Air Population

NASA Astrophysics Data System (ADS)

Peterson, Michael P.; Hunt, Paul; Weiß, Konrad

2018-05-01

"Air population" refers to the total number of people flying above the earth at any point in time. The total number of passengers can then be estimated by multiplying the number of seats for each aircraft by the current seat occupancy rate. Using this method, the estimated air population is determined by state for the airspace over the United States. In the interactive, real-time mapping system, maps are provided to show total air population, the density of air population (air population / area of state), and the ratio of air population to ground population.

Genetic variation among natural and laboratory colony populations of Lutzomyia longipalpis (Lutz & Neiva, 1912)(Diptera: Psychodidae) from Colombia.

PubMed

Lanzaro, G C; Alexander, B; Mutebi, J P; Montoya-Lerma, J; Warburg, A

1998-01-01

Genetic diversity among three field populations of Lutzomyia longipalpis in Colombia was studied using isozyme analysis. Study sites were as much as 598 km apart and included populations separated by the eastern Cordillera of the Andes. Genetic variability among populations, estimated by heterozygosity, was within values typical for insects in general (8.1%). Heterozygosity for field populations were compared with a laboratory colony from Colombia (Melgar colony) and were only slightly lower. These results suggest that establishment and long term maintenance of the Melgar colony has had little effect on the level of isozyme variability it carries. Genetic divergences between populations was evaluated using estimates of genetic distance. Genetic divergence among the three field populations was low (D = 0.021), suggesting they represent local populations within a single species. Genetic distance between field populations and the Melgar colony was also low (D = 0.016), suggesting that this colony population does not depart significantly from natural populations. Finally, comparisons were made between Colombian populations and colonies from Brazil and Costa Rica. Genetic distance values were high between Colombian and both Brazil and Costa Rica colony populations (D = 0.199 and 0.098 respectively) providing additional support for our earlier report that populations from the three countries represent distinct species.

Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations.

PubMed

Goldschmidt, Felix; Regoes, Roland R; Johnson, David R

2017-09-01

Successive range expansions occur within all domains of life, where one population expands first (primary expansion) and one or more secondary populations then follow (secondary expansion). In general, genetic drift reduces diversity during range expansion. However, it is not clear whether the same effect applies during successive range expansion, mainly because the secondary population must expand into space occupied by the primary population. Here we used an experimental microbial model system to show that, in contrast to primary range expansion, successive range expansion promotes local population diversity. Because of mechanical constraints imposed by the presence of the primary population, the secondary population forms fractal-like dendritic structures. This divides the advancing secondary population into many small sub-populations and promotes intermixing between the primary and secondary populations. We further developed a mathematical model to simulate the formation of dendritic structures in the secondary population during succession. By introducing mutations in the primary or dendritic secondary populations, we found that mutations are more likely to accumulate in the dendritic secondary populations. Our results thus show that successive range expansion can promote intermixing over the short term and increase genetic diversity over the long term. Our results therefore have potentially important implications for predicting the ecological processes and evolutionary trajectories of microbial communities.

Geographical and functional-morphological variations of the skull in the gray-bellied squirrel.

PubMed

Endo, Hideki; Kimura, Junpei; Oshida, Tatsuo; Stafford, Brian J; Rerkamnuaychoke, Worawut; Nishida, Takao; Sasaki, Motoki; Hayashida, Akiko; Hayashi, Yoshihiro

2004-03-01

The geographical variations of the skulls were osteometrically examined in the gray-bellied squirrel (Callosciurus caniceps) from the populations of Korat, Ranong, southernmost Thailand, and Terutau Island. The skull size was larger in northern population than in the southern population in the continental mainland. The zoogeographical influences of the Isthmus of Kra remained unclear, since the plots from Korat population were intermingled with those from southernmost Thailand population in the principal component charts. Although Korat population has been thought to belong to north group, we suggest that Ranong and southernmost Thailand populations may contain individuals from both north and south groups separated by the ancient Kra barrier. Terutau Island population was similar to southernmost Thailand population in skull size, although Terutau population has been isolated in the island and separated from the south group of the Isthmus of Kra. In the proportional analysis the interorbital space was narrower and the binocular sense has been well-developed in Terutau population. It suggests that this population has been highly adapted to arboreal behavior. In contrast, the skull with larger interorbital space was more adaptive for terrestrial life in Korat population. The canonical discriminant analysis could clearly separate the four populations in the scattergrams of discriminant scores.

[Krigle estimation and its simulated sampling of Chilo suppressalis population density].

PubMed

Yuan, Zheming; Bai, Lianyang; Wang, Kuiwu; Hu, Xiangyue

2004-07-01

In order to draw up a rational sampling plan for the larvae population of Chilo suppressalis, an original population and its two derivative populations, random population and sequence population, were sampled and compared with random sampling, gap-range-random sampling, and a new systematic sampling integrated Krigle interpolation and random original position. As for the original population whose distribution was up to aggregative and dependence range in line direction was 115 cm (6.9 units), gap-range-random sampling in line direction was more precise than random sampling. Distinguishing the population pattern correctly is the key to get a better precision. Gap-range-random sampling and random sampling are fit for aggregated population and random population, respectively, but both of them are difficult to apply in practice. Therefore, a new systematic sampling named as Krigle sample (n = 441) was developed to estimate the density of partial sample (partial estimation, n = 441) and population (overall estimation, N = 1500). As for original population, the estimated precision of Krigle sample to partial sample and population was better than that of investigation sample. With the increase of the aggregation intensity of population, Krigel sample was more effective than investigation sample in both partial estimation and overall estimation in the appropriate sampling gap according to the dependence range.

Genetic diversity of the Tibetan antelope (Pantholops hodgsonii) population of Ladakh, India, its relationship with other populations and conservation implications.

PubMed

Ahmad, Khursheed; Kumar, Ved P; Joshi, Bheem Dutt; Raza, Mohamed; Nigam, Parag; Khan, Anzara Anjum; Goyal, Surendra P

2016-10-21

The Tibetan antelope (Pantholops hodgsonii), or chiru, is an endangered antelope, distributed in China [Xinjiang, Xizang, Qinghai, Zhuolaihu Lake (Breeding habitat)], and India (Aksai Chin and Ladakh). There is a global demand for the species prized wool, which is used in weaving shahtoosh shawls. Over the years, the population of the Tibetan antelope has drastically declined from more than a million to a few thousand individuals, mainly due to poaching. Field studies undertaken in Ladakh, India also indicated winter migration of the population to Tibet. Migration between winter and calving habitats is well established to be female-biased across the Qinghai Tibetan Plateau (QTP). For effective conservation planning, genetic characterization is considered the best way to understand the likely impact of threats for ensuring the long-term viability of the population. In this regard, genetic characteristics of all Chinese populations are well-studied using mitochondrial and microsatellite markers, but information is lacking for the Indian population. Therefore, using the control region marker, we document for the first time the genetic variation of the Indian population of the Tibetan antelope, the extent of migration and its relationships with other populations of China. The partial fragment of control region (259 bp) marker was successfully amplified in 30 Tibetan antelope samples that were collected from the Chang Chenmo Valley in eastern Ladakh, India. We also retrieved control region sequences (n = 88) available in the public domain from GenBank of different Chinese populations. Low levels of nucleotide (π; 0.004) and haplotype (hd; 0.543) diversity were observed in the Indian population when compared to Chinese populations (π = 0.01357-0.02048 and hd = 0.889-0.986). Commonly used indices (Tajima's D and Fu's Fs) were analyzed for inferring the demographic history of the Indian populations, and all values were negative indicating population expansion or demographic equilibrium, though nonsignificant. We observed five haplotypes in the Indian population, and these were not reported in previously studied populations of QTP. Bayesian-based phylogenetic analysis indicates the presence of four clades, however, the posterior probability support for three of these clades is weak (<0.5). Of these, the Indian population formed a distinct clade, whereas the Chinese populations exhibited shared haplotypes, and no geographic structure was observed. Median-joining network analysis was conducted for 46 haplotypes in the overall population, except the samples from India which showed a star-like topology. The Indian population is separated by one median vector from the Chinese population. The present study revealed the presence of different sub-clades in the Bayesian phylogenetic tree and five new haplotypes only in the Indian population or sampling location. Furthermore, in the phylogenetic tree, Indian haplotypes of Tibetan antelopes were clustered with the haplotype reported in the Chinese population of the Xinjiang region. Median-joining network analysis showed shared haplotypes pattern in all populations of QTP except the samples from India which showed new haplotypes. Given the presence of low nucleotide and haplotype diversity in eastern Ladakh populations and limited information available for populations of the western side in its range, we suggest to include genetic studies of Tibetan antelope populations around Aksai Chin (Fig. 1) under the proposed transboundary agenda between India and China and assess relationships with other populations. Such understanding would enable the planning of conservation strategies for ensuring long-term survival of westernmost populations in its range, and if required, it would establish connectivity with the other populations.

Morphological and genetic divergence in Swedish postglacial stickleback (Pungitius pungitius) populations

PubMed Central

2011-01-01

Background An important objective of evolutionary biology is to understand the processes that govern phenotypic variation in natural populations. We assessed patterns of morphological and genetic divergence among coastal and inland lake populations of nine-spined stickleback in northern Sweden. Coastal populations are either from the Baltic coast (n = 5) or from nearby coastal lakes (n = 3) that became isolated from the Baltic Sea (< 100 years before present, ybp). Inland populations are from freshwater lakes that became isolated from the Baltic approximately 10,000 ybp; either single species lakes without predators (n = 5), or lakes with a recent history of predation (n = 5) from stocking of salmonid predators (~50 ybp). Results Coastal populations showed little variation in 11 morphological traits and had longer spines per unit of body length than inland populations. Inland populations were larger, on average, and showed greater morphological variation than coastal populations. A principal component analysis (PCA) across all populations revealed two major morphological axes related to spine length (PC1, 47.7% variation) and body size (PC2, 32.9% variation). Analysis of PCA scores showed marked similarity in coastal (Baltic coast and coastal lake) populations. PCA scores indicate that inland populations with predators have higher within-group variance in spine length and lower within-group variance in body size than inland populations without predators. Estimates of within-group PST (a proxy for QST) from PCA scores are similar to estimates of FST for coastal lake populations but PST >FST for Baltic coast populations. PST >FST for PC1 and PC2 for inland predator and inland no predator populations, with the exception that PST

When bigger is not better: intraspecific competition for pollination increases with population size in invasive milkweeds.

PubMed

Ward, Megan; Johnson, Steven D; Zalucki, Myron P

2013-04-01

One of the essential requirements for an introduced plant species to become invasive is an ability to reproduce outside the native range, particularly when initial populations are small. If a reproductive Allee effect is operating, plants in small populations will have reduced reproductive success relative to plants in larger populations. Alternatively, if plants in small populations experience less competition for pollination than those in large populations, they may actually have higher levels of reproductive success than plants in large populations. To resolve this uncertainty, we investigated how the per capita fecundity of plants was affected by population size in three invasive milkweed species. Field surveys of seed production in natural populations of different sizes but similar densities were conducted for three pollinator-dependent invasive species, namely Asclepias curassavica, Gomphocarpus fruticosus and G. physocarpus. Additionally, supplemental hand-pollinations were performed in small and large populations in order to determine whether reproductive output was limited by pollinator activity in these populations. Reproductive Allee effects were not detected in any of the study species. Instead, plants in small populations exhibited remarkably high levels of reproductive output compared to those in large populations. Increased fruit production following supplemental hand-pollinations suggested that the lower reproductive output of naturally pollinated plants in large populations is a consequence of pollen limitation rather than limitation due to abiotic resources. This is consistent with increased intraspecific competition for pollination amongst plants in large populations. It is likely that the invasion of these milkweed species in Australia has been enhanced because plants in small founding populations experience less intraspecific competition for pollinators than those in large populations, and thus have the ability to produce copious amounts of seeds.

[On the relationship between population and means of subsistence].

PubMed

Li, J

1984-01-29

Population is the basis of all social activites and social production. Population growth and development must have a definite means of subsistence to meet its cultural and material needs. The larger the population of a country, the greater is its demand for consumer goods and, likewise, the yield of its means of subsistence should be greater. Population brings about the unification of production and consumption. Furthermore, the ratio of population to the means of subsistence must be maintained at an appropriate level. Population growth must be slower then the growth of the means of subsistence in order to ensure continuous economic expansion and population increase. However, there are some people, notably Malthus, who believe that the balance between population growth and the means of subsistence should be equal. It is crucial to note differences between Marxist and Malthusian points of view. The basic outlook on the nature of the relationship between population and the means of subsistence is different. For Malthusians, it is a matter of the number of people and the quantity of the means of subsistence. For Marxists, the relationship is a historically determined social relationship. For Malthusians, population development is the primary force behind social development, i.e., the imbalance between population and the means of subsistence stems from social ills. Marxists differ from this in believing that population cannot be divorced from material production. Malthusians believe that population surplus derives from a population increase that is greater than an increase in the means of subsistence. Marxists believe a population surplus is also an historically determined social relationship. The Malthusian outlook for the future of population and the means of subsistence is pessimistic, whereas the Marxian view embodies the optimism of revolution.

Evaluating models of population process in a threatened population of Steller’s eiders: A retrospective approach

USGS Publications Warehouse

Dunham, Kylee; Grand, James B.

2016-10-11

The Alaskan breeding population of Steller’s eiders (Polysticta stelleri) was listed as threatened under the Endangered Species Act in 1997 in response to perceived declines in abundance throughout their breeding and nesting range. Aerial surveys suggest the breeding population is small and highly variable in number, with zero birds counted in 5 of the last 25 years. Research was conducted to evaluate competing population process models of Alaskan-breeding Steller’s eiders through comparison of model projections to aerial survey data. To evaluate model efficacy and estimate demographic parameters, a Bayesian state-space modeling framework was used and each model was fit to counts from the annual aerial surveys, using sequential importance sampling and resampling. The results strongly support that the Alaskan breeding population experiences population level nonbreeding events and is open to exchange with the larger Russian-Pacific breeding population. Current recovery criteria for the Alaskan breeding population rely heavily on the ability to estimate population viability. The results of this investigation provide an informative model of the population process that can be used to examine future population states and assess the population in terms of the current recovery and reclassification criteria.

Evolution in Stage-Structured Populations

PubMed Central

Barfield, Michael; Holt, Robert D.; Gomulkiewicz, Richard

2016-01-01

For many organisms, stage is a better predictor of demographic rates than age. Yet no general theoretical framework exists for understanding or predicting evolution in stage-structured populations. Here, we provide a general modeling approach that can be used to predict evolution and demography of stage-structured populations. This advances our ability to understand evolution in stage-structured populations to a level previously available only for populations structured by age. We use this framework to provide the first rigorous proof that Lande’s theorem, which relates adaptive evolution to population growth, applies to stage-classified populations, assuming only normality and that evolution is slow relative to population dynamics. We extend this theorem to allow for different means or variances among stages. Our next major result is the formulation of Price’s theorem, a fundamental law of evolution, for stage-structured populations. In addition, we use data from Trillium grandiflorum to demonstrate how our models can be applied to a real-world population and thereby show their practical potential to generate accurate projections of evolutionary and population dynamics. Finally, we use our framework to compare rates of evolution in age- versus stage-structured populations, which shows how our methods can yield biological insights about evolution in stage-structured populations. PMID:21460563

Outbreaks, gene flow and effective population size in the migratory locust, Locusta migratoria: a regional-scale comparative survey.

PubMed

Chapuis, Marie-Pierre; Loiseau, Anne; Michalakis, Yannis; Lecoq, Michel; Franc, Alex; Estoup, Arnaud

2009-03-01

The potential effect of population outbreaks on within and between genetic variation of populations in pest species has rarely been assessed. In this study, we compare patterns of genetic variation in different sets of historically frequently outbreaking and rarely outbreaking populations of an agricultural pest of major importance, the migratory locust, Locusta migratoria. We analyse genetic variation within and between 24 populations at 14 microsatellites in Western Europe, where only ancient and low-intensity outbreaks have been reported (non-outbreaking populations), and in Madagascar and Northern China, where frequent and intense outbreak events have been recorded over the last century (outbreaking populations). Our comparative survey shows that (i) the long-term effective population size is similar in outbreaking and non-outbreaking populations, as evidenced by similar estimates of genetic diversity, and (ii) gene flow is substantially larger among outbreaking populations than among non-outbreaking populations, as evidenced by a fourfold to 30-fold difference in FST values. We discuss the implications for population dynamics and the consequences for management strategies of the observed patterns of genetic variation in L. migratoria populations with contrasting historical outbreak frequency and extent.

Injury risk in British Columbia, Canada, 1986 to 2009: are Aboriginal children and youth over-represented?

PubMed

George, M Anne; Jin, Andrew; Brussoni, Mariana; Lalonde, Christopher E; McCormick, Rod

2015-12-01

Children and youth worldwide are at high risk of injury resulting in morbidity, disability or mortality. Disparities in risk exist between and within countries, and by sex and ethnicity. Our aim is to contribute data on disparities of injury rates for Aboriginal children and youth compared with those of the general population in British Columbia (BC), Canada, by examining risks for the two populations, utilizing provincial administrative data over a 24-year period. Hospital discharge records from the provincial health care database for children and youth were used to identify injury for the years 1986 to 2009. Within the total BC population, the Aboriginal population was identified. Crude rates and standardized relative risks (SRR) of hospitalization were calculated, by year and category of injury type and external cause, and compared to the total BC population for males and females under age 25 years. Over the 24-year period, substantive decreases were found in hospitalization injury risks for children and youth in both Aboriginal and total populations, for both sexes, and for most categories and types of injuries. Risk in overall injury dropped by 69% for the Aboriginal population and by 66% for the total BC population, yet in every year, the Aboriginal population had a higher risk than the total BC population. There were over 70% declines in risks among females of intentionally inflicted injury by another, among both the Aboriginal and total BC populations. Risk of injury caused by transport vehicles has decreased by an overwhelming 83% and 72% for the Aboriginal male population and for the total BC male population, respectively. The over 70% declines in risks for females of intentionally inflicted injury by another, among both the Aboriginal and total BC populations is excellent news. Risk of injury caused by transport vehicles for males decreased overwhelmingly for both populations. Disparities in rates between the Aboriginal population and total BC population remain because of similarity in the proportional reductions among the two populations. Since the Aboriginal population started at a much higher risk, in absolute terms, the gap between the two populations is shrinking.

Development of genetic diversity, differentiation and structure over 500 years in four ponderosa pine populations.

PubMed

Lesser, M R; Parchman, T L; Jackson, S T

2013-05-01

Population history plays an important role in shaping contemporary levels of genetic variation and geographic structure. This is especially true in small, isolated range-margin populations, where effects of inbreeding, genetic drift and gene flow may be more pronounced than in large continuous populations. Effects of landscape fragmentation and isolation distance may have implications for persistence of range-margin populations if they are demographic sinks. We studied four small, disjunct populations of ponderosa pine over a 500-year period. We coupled demographic data obtained through dendroecological methods with microsatellite data to discern how and when contemporary levels of allelic diversity, among and within-population levels of differentiation, and geographic structure, arose. Alleles accumulated rapidly following initial colonization, demonstrating proportionally high levels of gene flow into the populations. At population sizes of approximately 100 individuals, allele accumulation saturated. Levels of genetic differentiation among populations (F(ST) and Jost's D(est)) and diversity within populations (F(IS)) remained stable through time. There was no evidence of geographic genetic structure at any time in the populations' history. Proportionally, high gene flow in the early stages of population growth resulted in rapid accumulation of alleles and quickly created relatively homogenous genetic patterns among populations. Our study demonstrates that contemporary levels of genetic diversity were formed quickly and early in population development. How contemporary genetic diversity accumulates over time is a key facet of understanding population growth and development. This is especially relevant given the extent and speed at which species ranges are predicted to shift in the coming century. © 2013 Blackwell Publishing Ltd.

Two decades of demography reveals that seed and seedling transitions limit population persistence in a translocated shrub

PubMed Central

Gross, C. L.; Mackay, D.

2014-01-01

Background and Aims Olearia flocktoniae is an endangered shrub that was passively translocated from its natural ecosystem, where it has since gone extinct. This study aimed to determine sensitivities vital to populations persisting in human-created areas. Methods Population colonization, longevity and extinction were investigated over 20 years using 133 populations. Seed-bank longevity was determined from germination trials of seeds exhumed from extinct and extant sites via a 10-year glasshouse trial and by in situ sowing experiments. From 27 populations, 98 cohorts were followed and matrix models of transitions from seeds to adults were used to evaluate the intrinsic rate of population growth against disturbance histories. Ten populations (38 cohorts) with different disturbance histories were used to evaluate sensitivities in vital rates. Key Results Most populations had few individuals (∼30) and were transient (<5 years above ground). The intrinsic population growth rate was rarely >1 and all but two populations were extinct at year 20. Seeds were short-lived in situ. Although >1000 seeds per plant were produced annually in most populations, sensitivity analysis showed that the transition to the seed bank and the transition from the seed bank to seedlings are key vulnerabilities in the life-cycle. Conclusions Seedling establishment is promoted by recent disturbance. Increasing the number of disturbance events in populations, even severe disturbances that almost extirpate populations, significantly increases longer-term population persistence. Only populations that were disturbed annually survived the full 20 years of the study. The results show that translocated populations of O. flocktoniae will fail to persist without active management. PMID:24844983

Cost-effectiveness analysis of HPV vaccination: comparing the general population with socially vulnerable individuals.

PubMed

Han, Kyu-Tae; Kim, Sun Jung; Lee, Seo Yoon; Park, Eun-Cheol

2014-01-01

After the WHO recommended HPV vaccination of the general population in 2009, government support of HPV vaccination programs was increased in many countries. However, this policy was not implemented in Korea due to perceived low cost-effectiveness. Thus, the aim of this study was to analyze the cost-utility of HPV vaccination programs targeted to high risk populations as compared to vaccination programs for the general population. Each study population was set to 100,000 people in a simulation study to determine the incremental cost-utility ratio (ICUR), then standard prevalence rates, cost, vaccination rates, vaccine efficacy, and the Quality-Adjusted Life-Years (QALYs) were applied to the analysis. In addition, sensitivity analysis was performed by assuming discounted vaccination cost. In the socially vulnerable population, QALYs gained through HPV vaccination were higher than that of the general population (General population: 1,019, Socially vulnerable population: 5,582). The results of ICUR showed that the cost of HPV vaccination was higher for the general population than the socially vulnerable population. (General population: 52,279,255 KRW, Socially vulnerable population: 9,547,347 KRW). Compared with 24 million KRW/QALYs as the social threshold, vaccination of the general population was not cost-effective. In contrast, vaccination of the socially vulnerable population was strongly cost-effective. The results suggest the importance and necessity of government support of HPV vaccination programs targeted to socially vulnerable populations because a targeted approach is much more cost-effective. The implementation of government support for such vaccination programs is a critical strategy for decreasing the burden of HPV infection in Korea.

Population growth enhances the mean fixation time of neutral mutations and the persistence of neutral variation.

PubMed

Waxman, D

2012-06-01

A fundamental result of population genetics states that a new mutation, at an unlinked neutral locus in a randomly mating diploid population, has a mean time of fixation of ∼4N(e) generations, where N(e) is the effective population size. This result is based on an assumption of fixed population size, which does not universally hold in natural populations. Here, we analyze such neutral fixations in populations of changing size within the framework of the diffusion approximation. General expressions are derived for the mean and variance of the fixation time in changing populations. Some explicit results are given for two cases: (i) the effective population size undergoes a sudden change, representing a sudden population expansion or a sudden bottleneck; (ii) the effective population changes linearly for a limited period of time and then remains constant. Additionally, a lower bound for the mean time of fixation is obtained for an effective population size that increases with time, and this is applied to exponentially growing populations. The results obtained in this work show, among other things, that for populations that increase in size, the mean time of fixation can be enhanced, sometimes substantially so, over 4N(e,0) generations, where N(e,0) is the effective population size at the time the mutation arises. Such an enhancement is associated with (i) an increased probability of neutral polymorphism in a population and (ii) an enhanced persistence of high-frequency neutral variation, which is the variation most likely to be observed.

Temporal analysis of genetic structure to assess population dynamics of reintroduced swift foxes.

PubMed

Cullingham, Catherine I; Moehrenschlager, Axel

2013-12-01

Reintroductions are increasingly used to reestablish species, but a paucity of long-term postrelease monitoring has limited understanding of whether and when viable populations subsequently persist. We conducted temporal genetic analyses of reintroduced populations of swift foxes (Vulpes velox) in Canada (Alberta and Saskatchewan) and the United States (Montana). We used samples collected 4 years apart, 17 years from the initiation of the reintroduction, and 3 years after the conclusion of releases. To assess program success, we genotyped 304 hair samples, subsampled from the known range in 2000 and 2001, and 2005 and 2006, at 7 microsatellite loci. We compared diversity, effective population size, and genetic connectivity over time in each population. Diversity remained stable over time and there was evidence of increasing effective population size. We determined population structure in both periods after correcting for differences in sample sizes. The geographic distribution of these populations roughly corresponded with the original release locations, which suggests the release sites had residual effects on the population structure. However, given that both reintroduction sites had similar source populations, habitat fragmentation, due to cropland, may be associated with the population structure we found. Although our results indicate growing, stable populations, future connectivity analyses are warranted to ensure both populations are not subject to negative small-population effects. Our results demonstrate the importance of multiple sampling years to fully capture population dynamics of reintroduced populations. Análisis Temporal de la Estructura Genética para Evaluar la Dinámica Poblacional de Zorros (Vulpes velox) Reintroducidos. © 2013 Society for Conservation Biology.

Detecting population recovery using gametic disequilibrium-based effective population size estimates

Treesearch

David A. Tallmon; Robin S. Waples; Dave Gregovich; Michael K. Schwartz

2012-01-01

Recovering populations often must meet specific growth rate or abundance targets before their legal status can be changed from endangered or threatened. While the efficacy, power, and performance of population metrics to infer trends in declining populations has received considerable attention, how these same metrics perform when populations are increasing is less...

Global Population Profile: 2002. International Population Reports

ERIC Educational Resources Information Center

Christenson, Matthew; McDevitt, Thomas; Stanecki, Karen

2004-01-01

Global Population Profile: 2002 summarizes the most important trends in global population at the dawn of the 21st century. The presentation is organized around four themes: (1) Global Population; (2) Growth, Global Population; (3) Composition, Contraceptive Prevalence in the Developing World; and (4) the AIDS Pandemic in the 21st Century. This…

7 CFR 1740.8 - Scoring criteria for the grant competition.

Code of Federal Regulations, 2013 CFR

2013-01-01

... follows: (1) The rural population of a core coverage area must be calculated. The rural population of a county is calculated by subtracting the county's urban population(s) from the total county population. If the core coverage area consists of multiple counties, the rural population is the sum of all included...

7 CFR 1740.8 - Scoring criteria for the grant competition.

Code of Federal Regulations, 2014 CFR

2014-01-01

... follows: (1) The rural population of a core coverage area must be calculated. The rural population of a county is calculated by subtracting the county's urban population(s) from the total county population. If the core coverage area consists of multiple counties, the rural population is the sum of all included...

7 CFR 1740.8 - Scoring criteria for the grant competition.

Code of Federal Regulations, 2012 CFR

2012-01-01

... follows: (1) The rural population of a core coverage area must be calculated. The rural population of a county is calculated by subtracting the county's urban population(s) from the total county population. If the core coverage area consists of multiple counties, the rural population is the sum of all included...

7 CFR 1740.8 - Scoring criteria for the grant competition.

Code of Federal Regulations, 2011 CFR

2011-01-01

... follows: (1) The rural population of a core coverage area must be calculated. The rural population of a county is calculated by subtracting the county's urban population(s) from the total county population. If the core coverage area consists of multiple counties, the rural population is the sum of all included...

Farm Population of the United States: 1976. Current Population Reports: Farm Population.

ERIC Educational Resources Information Center

Banks, Vera J.; And Others

Prepared cooperatively by the Bureau of the Census and the Economic Research Service of the U.S. DeparLment of Agriculture, this document presents narrative and tabular data on: demographic and social characteristics of the farm population; economic characteristics of the farm population; revision of farm population processing procedures; and…

Quantifying inter- and intra-population niche variability using hierarchical bayesian stable isotope mixing models.

PubMed

Semmens, Brice X; Ward, Eric J; Moore, Jonathan W; Darimont, Chris T

2009-07-09

Variability in resource use defines the width of a trophic niche occupied by a population. Intra-population variability in resource use may occur across hierarchical levels of population structure from individuals to subpopulations. Understanding how levels of population organization contribute to population niche width is critical to ecology and evolution. Here we describe a hierarchical stable isotope mixing model that can simultaneously estimate both the prey composition of a consumer diet and the diet variability among individuals and across levels of population organization. By explicitly estimating variance components for multiple scales, the model can deconstruct the niche width of a consumer population into relevant levels of population structure. We apply this new approach to stable isotope data from a population of gray wolves from coastal British Columbia, and show support for extensive intra-population niche variability among individuals, social groups, and geographically isolated subpopulations. The analytic method we describe improves mixing models by accounting for diet variability, and improves isotope niche width analysis by quantitatively assessing the contribution of levels of organization to the niche width of a population.

Group selections among laboratory populations of Tribolium.

PubMed

Wade, M J

1976-12-01

Selection at the population level or group selection is defined as genetic change that is brought about or maintained by the differential extinction and/or proliferation of populations. Group selection for both increased and decreased adult population size was carried out among laboratory populations of Tribolium castaneum at 37-day intervals. The effect of individual selection within populations on adult population size was evaluated in an additional control series of populations. The response in the group selection treatments occurred rapidly, within three or four generations, and was large in magnitude, at times differing from the controls by over 200%. This response to selection at the populational level occurred despite strong individual selection which caused a decline in the mean size of the control populations from over 200 adults to near 50 adults in nine 37-day intervals. "Assay" experiments indicated that selective changes in fecundity, developmental time, body weight, and cannibalism rates were responsible in part for the observed treatment differences in adult population size. These findings have implications in terms of speciation in organisms whose range is composed of many partially isolated local populations.

Both population size and patch quality affect local extinctions and colonizations.

PubMed

Franzén, Markus; Nilsson, Sven G

2010-01-07

Currently, the habitat of many species is fragmented, resulting in small local populations with individuals occasionally dispersing between the remaining habitat patches. In a solitary bee metapopulation, extinction probability was related to both local bee population sizes and pollen resources measured as host plant population size. Patch size, on the other hand, had no additional predictive power. The turnover rate of local bee populations in 63 habitat patches over 4 years was high, with 72 extinction events and 31 colonization events, but the pollen plant population was stable with no extinctions or colonizations. Both pollen resources and bee populations had strong and independent effects on extinction probability, but connectivity was not of importance. Colonizations occurred more frequently within larger host plant populations. For metapopulation survival of the bee, large pollen plant populations are essential, independent of current bee population size.

Role of patch size, disease, and movement in rapid extinction of bighorn sheep

USGS Publications Warehouse

Singer, F.J.; Zeigenfuss, L.C.; Spicer, L.

2001-01-01

The controversy (Berger 1990, 1999; Wehausen 1999) over rapid extinction in bighorn sheep (Ovis canadensis) has focused on population size alone as a correlate to persistence time. We report on the persistence and population performance of 24 translocated populations of bighorn sheep. Persistence in these sheep was strongly correlated with larger patch sizes, greater distance to domestic sheep, higher population growth rates, and migratory movements, as well as to larger population sizes. Persistence was also positively correlated with larger average home-range size (p = 0.058, n = 10 translocated populations) and home-range size of rams (p = 0.087, n = 8 translocated populations). Greater home-range size and dispersal rates of bighorn sheep were positively correlated to larger patches. We conclude that patch size and thus habitat carrying capacity, not population size per se, is the primary correlate to both population performance and persistence. Because habitat carrying capacity defines the upper limit to population size, clearly the amount of suitable habitat in a patch is ultimately linked to population size. Larger populations (250+ animals) were more likely to recover rapidly to their pre-epizootic survey number following an epizootic (p = 0.019), although the proportion of the population dying in the epizootic also influenced the probability of recovery (p = 0.001). Expensive management efforts to restore or increase bighorn sheep populations should focus on large habitat patches located ≥23 km from domestic sheep, and less effort should be expended on populations in isolated, small patches of habitat.

Effects of an invasive plant on population dynamics in toads.

PubMed

Greenberg, Daniel A; Green, David M

2013-10-01

When populations decline in response to unfavorable environmental change, the dynamics of their population growth shift. In populations that normally exhibit high levels of variation in recruitment and abundance, as do many amphibians, declines may be difficult to identify from natural fluctuations in abundance. However, the onset of declines may be evident from changes in population growth rate in sufficiently long time series of population data. With data from 23 years of study of a population of Fowler's toad (Anaxyrus [ = Bufo] fowleri) at Long Point, Ontario (1989-2011), we sought to identify such a shift in dynamics. We tested for trends in abundance to detect a change point in population dynamics and then tested among competing population models to identify associated intrinsic and extrinsic factors. The most informative models of population growth included terms for toad abundance and the extent of an invasive marsh plant, the common reed (Phragmites australis), throughout the toads' marshland breeding areas. Our results showed density-dependent growth in the toad population from 1989 through 2002. After 2002, however, we found progressive population decline in the toads associated with the spread of common reeds and consequent loss of toad breeding habitat. This resulted in reduced recruitment and population growth despite the lack of significant loss of adult habitat. Our results underscore the value of using long-term time series to identify shifts in population dynamics coincident with the advent of population decline. © 2013 Society for Conservation Biology.

Natural selection and neutral evolution jointly drive population divergence between alpine and lowland ecotypes of the allopolyploid plant Anemone multifida (Ranunculaceae).

PubMed

McEwen, Jamie R; Vamosi, Jana C; Rogers, Sean M

2013-01-01

Population differentiation can be driven in large part by natural selection, but selectively neutral evolution can play a prominent role in shaping patters of population divergence. The decomposition of the evolutionary history of populations into the relative effects of natural selection and selectively neutral evolution enables an understanding of the causes of population divergence and adaptation. In this study, we examined heterogeneous genomic divergence between alpine and lowland ecotypes of the allopolyploid plant, Anemone multifida. Using peak height and dominant AFLP data, we quantified population differentiation at non-outlier (neutral) and outlier loci to determine the potential contribution of natural selection and selectively neutral evolution to population divergence. We found 13 candidate loci, corresponding to 2.7% of loci, with signatures of divergent natural selection between alpine and lowland populations and between alpine populations (Fst  = 0.074-0.445 at outlier loci), but neutral population differentiation was also evident between alpine populations (FST  = 0.041-0.095 at neutral loci). By examining population structure at both neutral and outlier loci, we determined that the combined effects of selection and neutral evolution are associated with the divergence of alpine populations, which may be linked to extreme abiotic conditions and isolation between alpine sites. The presence of outlier levels of genetic variation in structured populations underscores the importance of separately analyzing neutral and outlier loci to infer the relative role of divergent natural selection and neutral evolution in population divergence.

Type 2 diabetes mellitus: distribution of genetic markers in Kazakh population

PubMed Central

Sikhayeva, Nurgul; Talzhanov, Yerkebulan; Iskakova, Aisha; Dzharmukhanov, Jarkyn; Nugmanova, Raushan; Zholdybaeva, Elena; Ramanculov, Erlan

2018-01-01

Background Ethnic differences exist in the frequencies of genetic variations that contribute to the risk of common disease. This study aimed to analyse the distribution of several genes, previously associated with susceptibility to type 2 diabetes and obesity-related phenotypes, in a Kazakh population. Methods A total of 966 individuals belonging to the Kazakh ethnicity were recruited from an outpatient clinic. We genotyped 41 common single nucleotide polymorphisms (SNPs) previously associated with type 2 diabetes in other ethnic groups and 31 of these were in Hardy–Weinberg equilibrium. The obtained allele frequencies were further compared to publicly available data from other ethnic populations. Allele frequencies for other (compared) populations were pooled from the haplotype map (HapMap) database. Principal component analysis (PCA), cluster analysis, and multidimensional scaling (MDS) were used for the analysis of genetic relationship between the populations. Results Comparative analysis of allele frequencies of the studied SNPs showed significant differentiation among the studied populations. The Kazakh population was grouped with Asian populations according to the cluster analysis and with the Caucasian populations according to PCA. According to MDS, results of the current study show that the Kazakh population holds an intermediate position between Caucasian and Asian populations. Conclusion A high percentage of population differentiation was observed between Kazakh and world populations. The Kazakh population was clustered with Caucasian populations, and this result may indicate a significant Caucasian component in the Kazakh gene pool. PMID:29551892

Genetic analysis of haplotype data for 23 Y-chromosome short tandem repeat loci in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina.

PubMed

Dogan, Serkan; Primorac, Dragan; Marjanović, Damir

2014-10-01

To explore the distribution and polymorphisms of 23 short tandem repeat (STR) loci on the Y chromosome in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina and to investigate its genetic relationships with the homeland Turkish population and neighboring populations. This study included 100 healthy unrelated male individuals from the Turkish population living in Sarajevo. Buccal swab samples were collected as a DNA source. Genomic DNA was extracted using the salting out method and amplification was performed using PowerPlex Y 23 amplification kit. The studied population was compared to other populations using pairwise genetic distances, which were represented with a multi-dimensional scaling plot. Haplotype and allele frequencies of the sample population were calculated and the results showed that all 100 samples had unique haplotypes. The most polymorphic locus was DYS458, and the least polymorphic DYS391. The observed haplotype diversity was 1.0000 ± 0.0014, with a discrimination capacity of 1.00 and the match probability of 0.01. Rst values showed that our sample population was closely related in both dimensions to the Lebanese and Iraqi populations, while it was more distant from Bosnian, Croatian, and Macedonian populations. Turkish population residing in Sarajevo could be observed as a representative Turkish population, since our results were consistent with those previously published for the homeland Turkish population. Also, this study once again proved that geographically close populations were genetically more related to each other.

Environmental variability and population dynamics: Do European and North American ducks play by the same rules?

USGS Publications Warehouse

Pöysä, Hannu; Rintala, Jukka; Johnson, Douglas H.; Kauppinen, Jukka; Lammi, Esa; Nudds, Thomas D.; Väänänen, Veli-Matti

2016-01-01

Density dependence, population regulation, and variability in population size are fundamental population processes, the manifestation and interrelationships of which are affected by environmental variability. However, there are surprisingly few empirical studies that distinguish the effect of environmental variability from the effects of population processes. We took advantage of a unique system, in which populations of the same duck species or close ecological counterparts live in highly variable (north American prairies) and in stable (north European lakes) environments, to distinguish the relative contributions of environmental variability (measured as between-year fluctuations in wetland numbers) and intraspecific interactions (density dependence) in driving population dynamics. We tested whether populations living in stable environments (in northern Europe) were more strongly governed by density dependence than populations living in variable environments (in North America). We also addressed whether relative population dynamical responses to environmental variability versus density corresponded to differences in life history strategies between dabbling (relatively “fast species” and governed by environmental variability) and diving (relatively “slow species” and governed by density) ducks. As expected, the variance component of population fluctuations caused by changes in breeding environments was greater in North America than in Europe. Contrary to expectations, however, populations in more stable environments were not less variable nor clearly more strongly density dependent than populations in highly variable environments. Also, contrary to expectations, populations of diving ducks were neither more stable nor stronger density dependent than populations of dabbling ducks, and the effect of environmental variability on population dynamics was greater in diving than in dabbling ducks. In general, irrespective of continent and species life history, environmental variability contributed more to variation in species abundances than did density. Our findings underscore the need for more studies on populations of the same species in different environments to verify the generality of current explanations about population dynamics and its association with species life history.

Effects of population succession on demographic and genetic processes: predictions and tests in the daylily Hemerocallis thunbergii (Liliaceae).

PubMed

Chung, Mi Yoon; Nason, John D; Chung, Myong Gi

2007-07-01

Spatial genetic structure within plant populations is influenced by variation in demographic processes through space and time, including a population's successional status. To determine how demographic structure and fine-scale genetic structure (FSGS) change with stages in a population's successional history, we studied Hemerocallis thunbergii (Liliaceae), a nocturnal flowering and hawkmoth-pollinated herbaceous perennial with rapid population turnover dynamics. We examined nine populations assigned to three successive stages of population succession: expansion, maturation, and senescence. We developed stage-specific expectations for within-population demographic and genetic structure, and then for each population quantified the spatial aggregation of individuals and genotypes using spatial autocorrelation methods (nonaccumulative O-ring and kinship statistics, respectively), and at the landscape level measured inbreeding and genetic structure using Wright's F-statistics. Analyses using the O-ring statistic revealed significant aggregation of individuals at short spatial scales in expanding and senescing populations, in particular, which may reflect restricted seed dispersal around maternal individuals combined with relatively low local population densities at these stages. Significant FSGS was found for three of four expanding, no mature, and only one senescing population, a pattern generally consistent with expectations of successional processes. Although allozyme genetic diversity was high within populations (mean %P = 78.9 and H(E) = 0.281), landscape-level differentiation among sites was also high (F(ST) = 0.166) and all populations exhibited a significant deficit of heterozygotes relative to Hardy-Weinberg expectations (range F = 0.201-0.424, mean F(IS) = 0.321). Within populations, F was not correlated with the degree of FSGS, thus suggesting inbreeding due primarily to selfing as opposed to mating among close relatives in spatially structured populations. Our results demonstrate considerable variation in the spatial distribution of individuals and patterns and magnitude of FSGS in H. thunbergii populations across the landscape. This variation is generally consistent with succession-stage-specific differences in ecological processes operating within these populations.

Toxicological and biochemical characterizations of AChE in phosalone-susceptible and resistant populations of the common pistachio psyllid, Agonoscena pistaciae

PubMed Central

Alizadeh, Ali; Talebi-Jahromi, Khalil; Hosseininaveh, Vahid; Ghadamyari, Mohammad

2014-01-01

Abstract The toxicological and biochemical characteristics of acetylcholinesterases (AChE) in nine populations of the common pistachio psyllid, Agonoscena pistaciae Burckhardt and Lauterer (Hemiptera: Psyllidae), were investigated in Kerman Province, Iran. Nine A. pistaciae populations were collected from pistachio orchards, Pistacia vera L. (Sapindales: Anacardiaceae), located in Rafsanjan, Anar, Bam, Kerman, Shahrbabak, Herat, Sirjan, Pariz, and Paghaleh regions of Kerman province. The previous bioassay results showed these populations were susceptible or resistant to phosalone, and the Rafsanjan population was most resistant, with a resistance ratio of 11.3. The specific activity of AChE in the Rafsanjan population was significantly higher than in the susceptible population (Bam). The affinity ( KM ) and hydrolyzing efficiency ( Vmax ) of AChE on acetylthiocholine iodide, butyrylthiocholine iodide, and propionylthiocholine odide as artificial substrates were clearly lower in the Bam population than that in the Rafsanjan population. These results indicated that the AChE of the Rafsanjan population had lower affinity to these substrates than that of the susceptible population. The higher Vmax value in the Rafsanjan population compared to the susceptible population suggests a possible over expression of AChE in the Rafsanjan population. The in vitro inhibitory effect of several organophosphates and carbamates on AChE of the Rafsanjan and Bam populations was determined. Based on I50, the results showed that the ratios of AChE insensitivity of the resistant to susceptible populations were 23 and 21.7-fold to monocrotophos and phosphamidon, respectively. Whereas, the insensitivity ratios for Rafsanjan population were 0.86, 0.8, 0.78, 0.46, and 0.43 for carbaryl, eserine, propoxur, m-tolyl methyl carbamate, and carbofuran, respectively, suggesting negatively correlated sensitivity to organophosphate-insensitive AChE. Therefore, AChE from the Rafsanjan population showed negatively correlated sensitivity, being insensitive to phosphamidon and monocrotophos and sensitive to N -methyl carbamates. PMID:25373165

Estimating total population size for adult female sea turtles: Accounting for non-nesters

USGS Publications Warehouse

Kendall, W.L.; Richardson, J.I.; Rees, Alan F.

2008-01-01

Assessment of population size and changes therein is important to sea turtle management and population or life history research. Investigators might be interested in testing hypotheses about the effect of current population size or density (number of animals per unit resource) on future population processes. Decision makers might want to determine a level of allowable take of individual turtles of specified life stage. Nevertheless, monitoring most stages of sea turtle life histories is difficult, because obtaining access to individuals is difficult. Although in-water assessments are becoming more common, nesting females and their hatchlings remain the most accessible life stages. In some cases adult females of a given nesting population are sufficiently philopatric that the population itself can be well defined. If a well designed tagging study is conducted on this population, survival, breeding probability, and the size of the nesting population in a given year can be estimated. However, with published statistical methodology the size of the entire breeding population (including those females skipping nesting in that year) cannot be estimated without assuming that each adult female in this population has the same probability of nesting in a given year (even those that had just nested in the previous year). We present a method for estimating the total size of a breeding population (including nesters those skipping nesting) from a tagging study limited to the nesting population, allowing for the probability of nesting in a given year to depend on an individual's nesting status in the previous year (i.e., a Markov process). From this we further develop estimators for rate of growth from year to year in both nesting population and total breeding population, and the proportion of the breeding population that is breeding in a given year. We also discuss assumptions and apply these methods to a breeding population of hawksbill sea turtles (Eretmochelys imbricata) from the Caribbean. We anticipate that this method could also be useful for in-water studies of well defined populations.

Environmental variability and population dynamics: do European and North American ducks play by the same rules?

PubMed

Pöysä, Hannu; Rintala, Jukka; Johnson, Douglas H; Kauppinen, Jukka; Lammi, Esa; Nudds, Thomas D; Väänänen, Veli-Matti

2016-10-01

Density dependence, population regulation, and variability in population size are fundamental population processes, the manifestation and interrelationships of which are affected by environmental variability. However, there are surprisingly few empirical studies that distinguish the effect of environmental variability from the effects of population processes. We took advantage of a unique system, in which populations of the same duck species or close ecological counterparts live in highly variable (north American prairies) and in stable (north European lakes) environments, to distinguish the relative contributions of environmental variability (measured as between-year fluctuations in wetland numbers) and intraspecific interactions (density dependence) in driving population dynamics. We tested whether populations living in stable environments (in northern Europe) were more strongly governed by density dependence than populations living in variable environments (in North America). We also addressed whether relative population dynamical responses to environmental variability versus density corresponded to differences in life history strategies between dabbling (relatively "fast species" and governed by environmental variability) and diving (relatively "slow species" and governed by density) ducks. As expected, the variance component of population fluctuations caused by changes in breeding environments was greater in North America than in Europe. Contrary to expectations, however, populations in more stable environments were not less variable nor clearly more strongly density dependent than populations in highly variable environments. Also, contrary to expectations, populations of diving ducks were neither more stable nor stronger density dependent than populations of dabbling ducks, and the effect of environmental variability on population dynamics was greater in diving than in dabbling ducks. In general, irrespective of continent and species life history, environmental variability contributed more to variation in species abundances than did density. Our findings underscore the need for more studies on populations of the same species in different environments to verify the generality of current explanations about population dynamics and its association with species life history.

Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates

PubMed Central

Gill, Mandev S.; Lemey, Philippe; Bennett, Shannon N.; Biek, Roman; Suchard, Marc A.

2016-01-01

Effective population size characterizes the genetic variability in a population and is a parameter of paramount importance in population genetics and evolutionary biology. Kingman’s coalescent process enables inference of past population dynamics directly from molecular sequence data, and researchers have developed a number of flexible coalescent-based models for Bayesian nonparametric estimation of the effective population size as a function of time. Major goals of demographic reconstruction include identifying driving factors of effective population size, and understanding the association between the effective population size and such factors. Building upon Bayesian nonparametric coalescent-based approaches, we introduce a flexible framework that incorporates time-varying covariates that exploit Gaussian Markov random fields to achieve temporal smoothing of effective population size trajectories. To approximate the posterior distribution, we adapt efficient Markov chain Monte Carlo algorithms designed for highly structured Gaussian models. Incorporating covariates into the demographic inference framework enables the modeling of associations between the effective population size and covariates while accounting for uncertainty in population histories. Furthermore, it can lead to more precise estimates of population dynamics. We apply our model to four examples. We reconstruct the demographic history of raccoon rabies in North America and find a significant association with the spatiotemporal spread of the outbreak. Next, we examine the effective population size trajectory of the DENV-4 virus in Puerto Rico along with viral isolate count data and find similar cyclic patterns. We compare the population history of the HIV-1 CRF02_AG clade in Cameroon with HIV incidence and prevalence data and find that the effective population size is more reflective of incidence rate. Finally, we explore the hypothesis that the population dynamics of musk ox during the Late Quaternary period were related to climate change. [Coalescent; effective population size; Gaussian Markov random fields; phylodynamics; phylogenetics; population genetics. PMID:27368344

Effect of experimental manipulation on survival and recruitment of feral pigs

USGS Publications Warehouse

Hanson, L.B.; Mitchell, M.S.; Grand, J.B.; Jolley, D.B.; Sparklin, B.D.; Ditchkoff, S.S.

2009-01-01

Lethal removal is commonly used to reduce the density of invasive-species populations, presuming it reduces population growth rate; the actual effect of lethal removal on the vital rates contributing to population growth, however, is rarely tested. We implemented a manipulative experiment of feral pig (Sus scrofa) populations at Fort Benning, Georgia, USA, to assess the demographic effects of harvest intensity. Using markrecapture data, we estimated annual survival, recruitment, and population growth rates of populations in a moderately harvested area and a heavily harvested area for 200406. Population growth rates did not differ between the populations. The top-ranked model for survival included a harvest intensity effect; model-averaged survival was lower for the heavily harvested population than for the moderately harvested population. Increased immigration and reproduction likely compensated for the increased mortality in the heavily harvested population. We conclude that compensatory responses in feral pig recruitment can limit the success of lethal control efforts. ?? 2009 CSIRO.

Analysis of genetic admixture in Uyghur using the 26 Y-STR loci system

PubMed Central

Bian, Yingnan; Zhang, Suhua; Zhou, Wei; Zhao, Qi; Siqintuya; Zhu, Ruxin; Wang, Zheng; Gao, Yuzhen; Hong, Jie; Lu, Daru; Li, Chengtao

2016-01-01

The Uyghur population has experienced extensive interaction with European and Eastern Asian populations historically. A set of high-resolution genetic markers could be useful to infer the genetic relationships between the Uyghur population and European and Asian populations. In this study we typed 100 unrelated Uyghur males living in southern Xinjiang at 26 Y-STR loci. Using the high-resolution 26 Y-STR loci system, we investigated genetic and phylogenetic relationship between the Uyghur population and 23 reference European or Asian populations. We found that the Uyghur population exhibited a genetic admixture of Eastern Asian and European populations, and had a slightly closer relationship with the selected European populations than the Eastern Asian populations. We also demonstrated that the 26 Y-STR loci system was potentially useful in forensic sciences because it has a large power of discrimination and rarely exhibits common haplotypes. However, ancestry inference of Uyghur samples could be challenging due to the admixed nature of the population. PMID:26842947

Use of Population Genetics to Assess the Ecology, Evolution, and Population Structure of Coccidioides

PubMed Central

Teixeira, Marcus M.

2016-01-01

During the past 20 years, a general picture of the genetic diversity and population structure of Coccidioides, the causal agent of coccidioidomycosis (Valley fever), has emerged. The genus consists of 2 genetically diverse species, C. immitis and C. posadasii, each of which contains 1 or more distinct populations with limited gene flow. Genotypic data indicate that C. immitis is divided into 2 subpopulations (central and southern California populations) and C. posadasii is divided into 3 subpopulations (Arizona, Mexico, and Texas/South America populations). However, admixture within and among these populations and the current paucity of environmental isolates limit our understanding of the population genetics of Coccidioides. We assessed population structure of Coccidioides in Arizona by analyzing 495 clinical and environmental isolates. Our findings confirm the population structure as previously described and indicate a finer scale population structure in Arizona. Environmental isolates appear to have higher genetic diversity than isolates from human patients. PMID:27191589

Long-term population cycles in human societies.

PubMed

Turchin, Peter

2009-04-01

Human population dynamics are usually conceptualized as either boundless growth or growth to an equilibrium. The implicit assumption underlying these paradigms is that any feedback processes regulating population density, if they exist, operate on a fast-time-scale, and therefore we do not expect to observe population oscillations in human population numbers. This review asks, are population processes in historical and prehistorical human populations characterized by second-order feedback loops, that is, regulation involving lags? If yes, then the implications for forecasting future population change are obvious--what may appear as inexplicable, exogenously driven reverses in population trends may actually be a result of feedbacks operating with substantial time lags. This survey of a variety of historical and archeological data indicates that slow oscillations in population numbers, with periods of roughly two to three centuries, are observed in a number of world regions and historical periods. Next, a potential explanation for this pattern, the demographic-structural theory, is discussed. Finally, the implications of these results for global population forecasts is discussed.

Analysis of genetic admixture in Uyghur using the 26 Y-STR loci system.

PubMed

Bian, Yingnan; Zhang, Suhua; Zhou, Wei; Zhao, Qi; Siqintuya; Zhu, Ruxin; Wang, Zheng; Gao, Yuzhen; Hong, Jie; Lu, Daru; Li, Chengtao

2016-02-04

The Uyghur population has experienced extensive interaction with European and Eastern Asian populations historically. A set of high-resolution genetic markers could be useful to infer the genetic relationships between the Uyghur population and European and Asian populations. In this study we typed 100 unrelated Uyghur males living in southern Xinjiang at 26 Y-STR loci. Using the high-resolution 26 Y-STR loci system, we investigated genetic and phylogenetic relationship between the Uyghur population and 23 reference European or Asian populations. We found that the Uyghur population exhibited a genetic admixture of Eastern Asian and European populations, and had a slightly closer relationship with the selected European populations than the Eastern Asian populations. We also demonstrated that the 26 Y-STR loci system was potentially useful in forensic sciences because it has a large power of discrimination and rarely exhibits common haplotypes. However, ancestry inference of Uyghur samples could be challenging due to the admixed nature of the population.

[On some characteristics of the population development in the Shenzhen Special Economic Region].

PubMed

Zhang, Z; Yang, Q; An, H; Fang, D

1984-03-29

Shenzhen was originally a town in Guandong Province. In 1979, it was made into a Special Economic Region in order to cope with the needs of modernization. Because of rapid economic development, the population has also been growing rapidly. Before 1979, the total population of Shenzhen was only 20,000, both industry and agriculture were backward, and the living standard was low. After it was made a Special Economic Region, its population figure reached 200,000 according to a 1982 report. The age structure of the local population is young, and there are more males than females. In the last two years, because of family planning measures, the natural population growth rate has shown an obvious downward trend. The population development of Shenzhen has several characteristics: 1) the pace of population growth is very fast; 2) the educational level for the population is high, and investment in education is emphasized; 3) population mobility is strong, and it has an extensive impact on the local market, transportation, and social order; 4) the social and economic systems of Hong Kong have a special influence on its population development. Special studies and discussions concerning how to control Shenzhen's population growth, how to determine the trends toward change in age structure, and how to promote population quality and spiritual civilization should be conducted according to characteristics of the local population development.

Correlation analysis of genetic diversity and population structure of Houttuynia cordata Thunb with regard to environment.

PubMed

Zhong, J; Wu, F-C; Qiu, P; Dai, L-J

2016-08-12

To study the levels of genetic diversity, and population structure, of Houttuynia cordata Thunb, the genetic background and relationships of populations were analyzed in terms of environmental factors. The genetic diversity and population structure of H. cordata were investigated using sequence-related amplified polymorphisms and correlation with environmental factors was analyzed using the SPSS software. Two thousand one hundred sixty-three sites were amplified from 41 pairs of primers, 1825 of which were polymorphic, and the percentage of polymorphic loci was 84.37%; the percentage of polymorphic sites was 72.14 and 67.77% at the species and population level, respectively. The observed number of alleles was 1.52 and 1.30 at species and population level, respectively. The effective number of alleles was 1.38 and 1.24 at species and population level, respectively. The Nei's diversity was 0.26 and 0.15 at species and population level, respectively. The Shannon's information index was 0.87 and 0.63 at species and population level, respectively. The genetic differentiation coefficient of populations was 0.51, and 12 populations were divided into three classes based on D = 0.20; the genetic diversities of different populations are correlated at different significance levels (P < 0.05) with environmental factors. Genetic differentiation existed among populations and the populations exhibited heteroplasmy.

Does colour polymorphism enhance survival of prey populations?

PubMed Central

Wennersten, Lena; Forsman, Anders

2009-01-01

That colour polymorphism may protect prey populations from predation is an old but rarely tested hypothesis. We examine whether colour polymorphic populations of prey exposed to avian predators in an ecologically valid visual context were exposed to increased extinction risk compared with monomorphic populations. We made 2976 artificial pastry prey, resembling Lepidoptera larvae, in four different colours and presented them in 124 monomorphic and 124 tetramorphic populations on tree trunks and branches such that they would be exposed to predation by free-living birds, and monitored their ‘survival’. Among monomorphic populations, there was a significant effect of prey coloration on survival, confirming that coloration influenced susceptibility to visually oriented predators. Survival of polymorphic populations was inferior to that of monomorphic green populations, but did not differ significantly from monomorphic brown, yellow or red populations. Differences in survival within polymorphic populations paralleled those seen among monomorphic populations; the red morph most frequently went extinct first and the green morph most frequently survived the longest. Our findings do not support the traditional protective polymorphism hypothesis and are in conflict with those of earlier studies. As a possible explanation to our findings, we offer a competing ‘giveaway cue’ hypothesis: that polymorphic populations may include one morph that attracts the attention of predators and that polymorphic populations therefore may suffer increased predation compared with some monomorphic populations. PMID:19324729

Different level of population differentiation among human genes.

PubMed

Wu, Dong-Dong; Zhang, Ya-Ping

2011-01-14

During the colonization of the world, after dispersal out of African, modern humans encountered changeable environments and substantial phenotypic variations that involve diverse behaviors, lifestyles and cultures, were generated among the different modern human populations. Here, we study the level of population differentiation among different populations of human genes. Intriguingly, genes involved in osteoblast development were identified as being enriched with higher FST SNPs, a result consistent with the proposed role of the skeletal system in accounting for variation among human populations. Genes involved in the development of hair follicles, where hair is produced, were also found to have higher levels of population differentiation, consistent with hair morphology being a distinctive trait among human populations. Other genes that showed higher levels of population differentiation include those involved in pigmentation, spermatid, nervous system and organ development, and some metabolic pathways, but few involved with the immune system. Disease-related genes demonstrate excessive SNPs with lower levels of population differentiation, probably due to purifying selection. Surprisingly, we find that Mendelian-disease genes appear to have a significant excessive of SNPs with high levels of population differentiation, possibly because the incidence and susceptibility of these diseases show differences among populations. As expected, microRNA regulated genes show lower levels of population differentiation due to purifying selection. Our analysis demonstrates different level of population differentiation among human populations for different gene groups.

75 FR 13484 - Renewal of the Census Advisory Committees on the Race and Ethnic Populations

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-22

... Asian Population, Census Advisory Committee on the Hispanic Populations and Census Advisory Committee on... Asian Population, Census Advisory Committee on the Hispanic Populations and Census Advisory Committee on...

GENETICS AND POPULATION-LEVEL RISK ASSESSMENT

EPA Science Inventory

Genetic variation defines population structure and provides the mechanism for populations to adapt to novel stressors. Despite its fundamental importance in understanding populations, genetic information has been included rarely in models of population dynamics (endangered speci...

Population Profile of the United States: 1976. Current Population Reports, Population Characteristics, Series P-20, No. 307.

ERIC Educational Resources Information Center

Bureau of the Census (DOC), Suitland, MD. Population Div.

This booklet summarizes population characteristics of the United States for 1976. A preliminary section of highlights reviews trends in five areas: population growth, social characteristics, population distribution, employment and income, and ethnic groups. The birth rate has declined, and the rate of childlessness has risen. This probably is due…

World Population: Toward the Next Century. Revised Edition.

ERIC Educational Resources Information Center

Murphy, Elaine M.

This document consists of answers to questions on various aspects of world population. They are: What is the population of the world? How fast is the population of the world growing? When will the population of the world stop growing? Is the term "population explosion" accurate? Why did this sudden growth occur? Did people have more babies than…

45 CFR Appendix C to Part 1356 - Calculating Sample Size for NYTD Follow-Up Populations

Code of Federal Regulations, 2012 CFR

2012-10-01

... Populations C Appendix C to Part 1356 Public Welfare Regulations Relating to Public Welfare (Continued) OFFICE... Follow-Up Populations 1. Using Finite Population Correction The Finite Population Correction (FPC) is applied when the sample is drawn from a population of one to 5,000 youth, because the sample is more than...

45 CFR Appendix C to Part 1356 - Calculating Sample Size for NYTD Follow-Up Populations

Code of Federal Regulations, 2014 CFR

2014-10-01

... Populations C Appendix C to Part 1356 Public Welfare Regulations Relating to Public Welfare (Continued) OFFICE... Follow-Up Populations 1. Using Finite Population Correction The Finite Population Correction (FPC) is applied when the sample is drawn from a population of one to 5,000 youth, because the sample is more than...

45 CFR Appendix C to Part 1356 - Calculating Sample Size for NYTD Follow-Up Populations

Code of Federal Regulations, 2011 CFR

2011-10-01

... Populations C Appendix C to Part 1356 Public Welfare Regulations Relating to Public Welfare (Continued) OFFICE... Follow-Up Populations 1. Using Finite Population Correction The Finite Population Correction (FPC) is applied when the sample is drawn from a population of one to 5,000 youth, because the sample is more than...

Estimation of effective population size in continuously distributed populations: There goes the neighborhood

Treesearch

M. C. Neel; K. McKelvey; N. Ryman; M. W. Lloyd; R. Short Bull; F. W. Allendorf; M. K. Schwartz; R. S. Waples

2013-01-01

Use of genetic methods to estimate effective population size (Ne) is rapidly increasing, but all approaches make simplifying assumptions unlikely to be met in real populations. In particular, all assume a single, unstructured population, and none has been evaluated for use with continuously distributed species. We simulated continuous populations with local mating...

Population modelling to compare chronic external radiotoxicity between individual and population endpoints in four taxonomic groups.

PubMed

Alonzo, Frédéric; Hertel-Aas, Turid; Real, Almudena; Lance, Emilie; Garcia-Sanchez, Laurent; Bradshaw, Clare; Vives I Batlle, Jordi; Oughton, Deborah H; Garnier-Laplace, Jacqueline

2016-02-01

In this study, we modelled population responses to chronic external gamma radiation in 12 laboratory species (including aquatic and soil invertebrates, fish and terrestrial mammals). Our aim was to compare radiosensitivity between individual and population endpoints and to examine how internationally proposed benchmarks for environmental radioprotection protected species against various risks at the population level. To do so, we used population matrix models, combining life history and chronic radiotoxicity data (derived from laboratory experiments and described in the literature and the FREDERICA database) to simulate changes in population endpoints (net reproductive rate R0, asymptotic population growth rate λ, equilibrium population size Neq) for a range of dose rates. Elasticity analyses of models showed that population responses differed depending on the affected individual endpoint (juvenile or adult survival, delay in maturity or reduction in fecundity), the considered population endpoint (R0, λ or Neq) and the life history of the studied species. Among population endpoints, net reproductive rate R0 showed the lowest EDR10 (effective dose rate inducing 10% effect) in all species, with values ranging from 26 μGy h(-1) in the mouse Mus musculus to 38,000 μGy h(-1) in the fish Oryzias latipes. For several species, EDR10 for population endpoints were lower than the lowest EDR10 for individual endpoints. Various population level risks, differing in severity for the population, were investigated. Population extinction (predicted when radiation effects caused population growth rate λ to decrease below 1, indicating that no population growth in the long term) was predicted for dose rates ranging from 2700 μGy h(-1) in fish to 12,000 μGy h(-1) in soil invertebrates. A milder risk, that population growth rate λ will be reduced by 10% of the reduction causing extinction, was predicted for dose rates ranging from 24 μGy h(-1) in mammals to 1800 μGy h(-1) in soil invertebrates. These predictions suggested that proposed reference benchmarks from the literature for different taxonomic groups protected all simulated species against population extinction. A generic reference benchmark of 10 μGy h(-1) protected all simulated species against 10% of the effect causing population extinction. Finally, a risk of pseudo-extinction was predicted from 2.0 μGy h(-1) in mammals to 970 μGy h(-1) in soil invertebrates, representing a slight but statistically significant population decline, the importance of which remains to be evaluated in natural settings. Copyright © 2015 Elsevier Ltd. All rights reserved.

Population-specific life histories contribute to metapopulation viability

USGS Publications Warehouse

Halsey, Samniqueka J.; Bell, Timothy J.; McEachern, A. Kathryn; Pavlovic, Noel B.

2016-01-01

Restoration efforts can be improved by understanding how variations in life-history traits occur within populations of the same species living in different environments. This can be done by first understanding the demographic responses of natural occurring populations. Population viability analysis continues to be useful to species management and conservation with sensitivity analysis aiding in the understanding of population dynamics. In this study, using life-table response experiments and elasticity analyses, we investigated how population-specific life-history demographic responses contributed to the metapopulation viability of the Federally threatened Pitcher's thistle (Cirsium pitcheri). Specifically, we tested the following hypotheses: (1) Subpopulations occupying different environments within a metapopulation have independent demographic responses and (2) advancing succession results in a shift from a demographic response focused on growth and fecundity to one dominated by stasis. Our results showed that reintroductions had a positive contribution to the metapopulation growth rate as compared to native populations which had a negative contribution. We found no difference in succession on the contribution to metapopulation viability. In addition, we identified distinct population-specific contributions to metapopulation viability and were able to associate specific life-history demographic responses. For example, the positive impact of Miller High Dunes population on the metapopulation growth rate resulted from high growth contributions, whereas increased time of plant in stasis for the State Park Big Blowout population resulted in negative contributions. A greater understanding of how separate populations respond in their corresponding environment may ultimately lead to more effective management strategies aimed at reducing extinction risk. We propose the continued use of sensitivity analyses to evaluate population-specific demographic influences on metapopulation viability. In understanding the underlying causes of the projected extinction probabilities of each population and identifying broad-scale contributions of different populations to the metapopulation, the process of pinpointing target populations is simplified. More detailed analyses can then be applied to the target populations to increase population viability and consequently metapopulation viability. Based on our research, we suggest that the best approach to improve the overall metapopulation viability is to manage the contributions to population growth for each population separately.

Microsatellite data suggest significant population structure and differentiation within the malaria vector Anopheles darlingi in Central and South America.

PubMed

Mirabello, Lisa; Vineis, Joseph H; Yanoviak, Stephen P; Scarpassa, Vera M; Póvoa, Marinete M; Padilla, Norma; Achee, Nicole L; Conn, Jan E

2008-03-26

Anopheles darlingi is the most important malaria vector in the Neotropics. An understanding of A. darlingi's population structure and contemporary gene flow patterns is necessary if vector populations are to be successfully controlled. We assessed population genetic structure and levels of differentiation based on 1,376 samples from 31 localities throughout the Peruvian and Brazilian Amazon and Central America using 5-8 microsatellite loci. We found high levels of polymorphism for all of the Amazonian populations (mean RS = 7.62, mean HO = 0.742), and low levels for the Belize and Guatemalan populations (mean RS = 4.3, mean HO = 0.457). The Bayesian clustering analysis revealed five population clusters: northeastern Amazonian Brazil, southeastern and central Amazonian Brazil, western and central Amazonian Brazil, Peruvian Amazon, and the Central American populations. Within Central America there was low non-significant differentiation, except for between the populations separated by the Maya Mountains. Within Amazonia there was a moderate level of significant differentiation attributed to isolation by distance. Within Peru there was no significant population structure and low differentiation, and some evidence of a population expansion. The pairwise estimates of genetic differentiation between Central America and Amazonian populations were all very high and highly significant (FST = 0.1859 - 0.3901, P < 0.05). Both the DA and FST distance-based trees illustrated the main division to be between Central America and Amazonia. We detected a large amount of population structure in Amazonia, with three population clusters within Brazil and one including the Peru populations. The considerable differences in Ne among the populations may have contributed to the observed genetic differentiation. All of the data suggest that the primary division within A. darlingi corresponds to two white gene genotypes between Amazonia (genotype 1) and Central America, parts of Colombia and Venezuela (genotype 2), and are in agreement with previously published mitochondrial COI gene sequences interpreted as incipient species. Overall, it appears that two main factors have contributed to the genetic differentiation between the population clusters: physical distance between the populations and the differences in effective population sizes among the subpopulations.

Andean Condor (Vultur gryphus) in Ecuador: Geographic Distribution, Population Size and Extinction Risk.

PubMed

Naveda-Rodríguez, Adrián; Vargas, Félix Hernán; Kohn, Sebastián; Zapata-Ríos, Galo

2016-01-01

The Andean Condor (Vultur gryphus) in Ecuador is classified as Critically Endangered. Before 2015, standardized and systematic estimates of geographic distribution, population size and structure were not available for this species, hampering the assessment of its current status and hindering the design and implementation of effective conservation actions. In this study, we performed the first quantitative assessment of geographic distribution, population size and population viability of Andean Condor in Ecuador. We used a methodological approach that included an ecological niche model to study geographic distribution, a simultaneous survey of 70 roosting sites to estimate population size and a population viability analysis (PVA) for the next 100 years. Geographic distribution in the form of extent of occurrence was 49 725 km2. During a two-day census, 93 Andean Condors were recorded and a population of 94 to 102 individuals was estimated. In this population, adult-to-immature ratio was 1:0.5. In the modeled PVA scenarios, the probability of extinction, mean time to extinction and minimum population size varied from zero to 100%, 63 years and 193 individuals, respectively. Habitat loss is the greatest threat to the conservation of Andean Condor populations in Ecuador. Population size reduction in scenarios that included habitat loss began within the first 15 years of this threat. Population reinforcement had no effects on the recovery of Andean Condor populations given the current status of the species in Ecuador. The population size estimate presented in this study is the lower than those reported previously in other countries where the species occur. The inferences derived from the population viability analysis have implications for Condor management in Ecuador. This study highlights the need to redirect efforts from captive breeding and population reinforcement to habitat conservation.

Andean Condor (Vultur gryphus) in Ecuador: Geographic Distribution, Population Size and Extinction Risk

PubMed Central

Naveda-Rodríguez, Adrián; Vargas, Félix Hernán; Kohn, Sebastián; Zapata-Ríos, Galo

2016-01-01

The Andean Condor (Vultur gryphus) in Ecuador is classified as Critically Endangered. Before 2015, standardized and systematic estimates of geographic distribution, population size and structure were not available for this species, hampering the assessment of its current status and hindering the design and implementation of effective conservation actions. In this study, we performed the first quantitative assessment of geographic distribution, population size and population viability of Andean Condor in Ecuador. We used a methodological approach that included an ecological niche model to study geographic distribution, a simultaneous survey of 70 roosting sites to estimate population size and a population viability analysis (PVA) for the next 100 years. Geographic distribution in the form of extent of occurrence was 49 725 km2. During a two-day census, 93 Andean Condors were recorded and a population of 94 to 102 individuals was estimated. In this population, adult-to-immature ratio was 1:0.5. In the modeled PVA scenarios, the probability of extinction, mean time to extinction and minimum population size varied from zero to 100%, 63 years and 193 individuals, respectively. Habitat loss is the greatest threat to the conservation of Andean Condor populations in Ecuador. Population size reduction in scenarios that included habitat loss began within the first 15 years of this threat. Population reinforcement had no effects on the recovery of Andean Condor populations given the current status of the species in Ecuador. The population size estimate presented in this study is the lower than those reported previously in other countries where the species occur. The inferences derived from the population viability analysis have implications for Condor management in Ecuador. This study highlights the need to redirect efforts from captive breeding and population reinforcement to habitat conservation. PMID:26986004

Patterns of Genetic Variation across Altitude in Three Plant Species of Semi-Dry Grasslands

PubMed Central

Hahn, Thomas; Kettle, Chris J.; Ghazoul, Jaboury; Frei, Esther R.; Matter, Philippe; Pluess, Andrea R.

2012-01-01

Background Environmental gradients caused by altitudinal gradients may affect genetic variation within and among plant populations and inbreeding within populations. Populations in the upper range periphery of a species may be important source populations for range shifts to higher altitude in response to climate change. In this study we investigate patterns of population genetic variation at upper peripheral and lower more central altitudes in three common plant species of semi-dry grasslands in montane landscapes. Methodology/Principal Findings In Briza media, Trifolium montanum and Ranunculus bulbosus genetic diversity, inbreeding and genetic relatedness of individuals within populations and genetic differentiation among populations was characterized using AFLP markers. Populations were sampled in the Swiss Alps at 1800 (upper periphery of the study organisms) and at 1200 m a.s.l. Genetic diversity was not affected by altitude and only in B. media inbreeding was greater at higher altitudes. Genetic differentiation was slightly greater among populations at higher altitudes in B. media and individuals within populations were more related to each other compared to individuals in lower altitude populations. A similar but less strong pattern of differentiation and relatedness was observed in T. montanum, while in R. bulbosus there was no effect of altitude. Estimations of population size and isolation of populations were similar, both at higher and lower altitudes. Conclusions/Significance Our results suggest that altitude does not affect genetic diversity in the grassland species under study. Genetic differentiation of populations increased only slightly at higher elevation, probably due to extensive (historic) gene flow among altitudes. Potentially pre-adapted genes might therefore spread easily across altitudes. Our study indicates that populations at the upper periphery are not genetically depauperate or isolated and thus may be important source populations for migration under climate change. PMID:22870236

Two decades of demography reveals that seed and seedling transitions limit population persistence in a translocated shrub.

PubMed

Gross, C L; Mackay, D

2014-07-01

Olearia flocktoniae is an endangered shrub that was passively translocated from its natural ecosystem, where it has since gone extinct. This study aimed to determine sensitivities vital to populations persisting in human-created areas. Population colonization, longevity and extinction were investigated over 20 years using 133 populations. Seed-bank longevity was determined from germination trials of seeds exhumed from extinct and extant sites via a 10-year glasshouse trial and by in situ sowing experiments. From 27 populations, 98 cohorts were followed and matrix models of transitions from seeds to adults were used to evaluate the intrinsic rate of population growth against disturbance histories. Ten populations (38 cohorts) with different disturbance histories were used to evaluate sensitivities in vital rates. Most populations had few individuals (∼30) and were transient (<5 years above ground). The intrinsic population growth rate was rarely >1 and all but two populations were extinct at year 20. Seeds were short-lived in situ. Although >1000 seeds per plant were produced annually in most populations, sensitivity analysis showed that the transition to the seed bank and the transition from the seed bank to seedlings are key vulnerabilities in the life-cycle. Seedling establishment is promoted by recent disturbance. Increasing the number of disturbance events in populations, even severe disturbances that almost extirpate populations, significantly increases longer-term population persistence. Only populations that were disturbed annually survived the full 20 years of the study. The results show that translocated populations of O. flocktoniae will fail to persist without active management. © The Author 2014. Published by Oxford University Press on behalf of the Annals of Botany Company.

Survival of Ranunculus repens L. (creeping buttercup) in an amphibious habitat.

PubMed

Lynn, D E; Waldren, S

2003-01-01

The turlough form of Ranunculus repens is subjected to several months' complete inundation with hard groundwater. Experimental flooding to the level of the soil surface had no effect on turlough or ruderal populations relative to drained controls. Experimental submergence resulted in direct tissue death of the ruderal population but did not affect the turlough population relative to drained controls. There was no detectable difference in the proportion of aerenchyma in drained, flooded and submerged roots of plants from either population. The proportion of aerenchyma increased with root age in the ruderal population. Up to twice the proportion of aerenchyma occurred in the lower third of the root in the turlough population relative to the middle and upper thirds. Submergence in artificially hardened tap water increased the amount of tissue death in the ruderal population, whereas it appeared to enhance the growth of plants from the turlough population relative to that of plants submerged in tap water. Only the ruderal population demonstrated a depth accommodation response in submerged conditions. Root concentrations of ethanol-soluble carbohydrates were up to three times higher in a field- collected turlough population during winter and autumn months than those in a ruderal population. Low levels of ethanol-insoluble carbohydrates were present in the turlough population but were absent from the ruderal population. Starch concentrations fluctuated greatly in the turlough population and were generally higher than those in the ruderal population. These results, together with those from previous investigations, suggest that the turlough population survives prolonged submergence by maintaining low levels of submerged photosynthesis, which may circulate oxygen within the plant tissues, and by utilizing storage carbohydrates for maintenance respiration. Copyright 2003 Annals of Botany Company

Genetic divergence and signatures of natural selection in marginal populations of a keystone, long-lived conifer, Eastern White Pine (Pinus strobus) from Northern Ontario.

PubMed

Chhatre, Vikram E; Rajora, Om P

2014-01-01

Marginal populations are expected to provide the frontiers for adaptation, evolution and range shifts of plant species under the anticipated climate change conditions. Marginal populations are predicted to show genetic divergence from central populations due to their isolation, and divergent natural selection and genetic drift operating therein. Marginal populations are also expected to have lower genetic diversity and effective population size (Ne) and higher genetic differentiation than central populations. We tested these hypotheses using eastern white pine (Pinus strobus) as a model for keystone, long-lived widely-distributed plants. All 614 eastern white pine trees, in a complete census of two populations each of marginal old-growth, central old-growth, and central second-growth, were genotyped at 11 microsatellite loci. The central populations had significantly higher allelic and genotypic diversity, latent genetic potential (LGP) and Ne than the marginal populations. However, heterozygosity and fixation index were similar between them. The marginal populations were genetically diverged from the central populations. Model testing suggested predominant north to south gene flow in the study area with curtailed gene flow to northern marginal populations. Signatures of natural selection were detected at three loci in the marginal populations; two showing divergent selection with directional change in allele frequencies, and one balancing selection. Contrary to the general belief, no significant differences were observed in genetic diversity, differentiation, LGP, and Ne between old-growth and second-growth populations. Our study provides information on the dynamics of migration, genetic drift and selection in central versus marginal populations of a keystone long-lived plant species and has broad evolutionary, conservation and adaptation significance.

Population genetic structure in Atlantic and Pacific Ocean common murres (Uria aalge): Natural replicate tests of post-Pleistocene evolution

USGS Publications Warehouse

Morris-Pocock, J. A.; Taylor, S.A.; Birt, T.P.; Damus, M.; Piatt, John F.; Warheit, K.I.; Friesen, Vicki L.

2008-01-01

Understanding the factors that influence population differentiation in temperate taxa can be difficult because the signatures of both historic and contemporary demographics are often reflected in population genetic patterns. Fortunately, analyses based on coalescent theory can help untangle the relative influence of these historic and contemporary factors. Common murres (Uria aalge) are vagile seabirds that breed in the boreal and low arctic waters of the Northern Hemisphere. Previous analyses revealed that Atlantic and Pacific populations are genetically distinct; however, less is known about population genetic structure within ocean basins. We employed the mitochondrial control region, four microsatellite loci and four intron loci to investigate population genetic structure throughout the range of common murres. As in previous studies, we found that Atlantic and Pacific populations diverged during the Pleistocene and do not currently exchange migrants. Therefore, Atlantic and Pacific murre populations can be used as natural replicates to test mechanisms of population differentiation. While we found little population genetic structure within the Pacific, we detected significant east-west structuring among Atlantic colonies. The degree that population genetic structure reflected contemporary population demographics also differed between ocean basins. Specifically, while the low levels of population differentiation in the Pacific are at least partially due to high levels of contemporary gene flow, the east-west structuring of populations within the Atlantic appears to be the result of historic fragmentation of populations rather than restricted contemporary gene flow. The contrasting results in the Atlantic and Pacific Oceans highlight the necessity of carefully considering multilocus nonequilibrium population genetic approaches when reconstructing the demographic history of temperate Northern Hemisphere taxa. ?? 2008 The Authors.

Population stress: A spatiotemporal analysis of population change and land development at the county level in the contiguous United States, 2001-2011.

PubMed

Chi, Guangqing; Ho, Hung Chak

2018-01-01

The past century has witnessed rapidly increasing population-land conflicts due to exponential population growth and its many consequences. Although the measures of population-land conflicts are many, there lacks a model that appropriately considers both the social and physical contexts of population-land conflicts. In this study we introduce the concept of population stress , which identifies areas with populations growing faster than the lands available for sustainable development. Specifically, population stress areas are identified by comparing population growth and land development as measured by land developability in the contiguous United States from 2001 to 2011. Our approach is based on a combination of spatial multicriteria analysis, zonal statistics, and spatiotemporal modeling. We found that the population growth of a county is associated with the decrease of land developability, along with the spatial influences of surrounding counties. The Midwest and the traditional "Deep South" counties would have less population stress with future land development, whereas the Southeast Coast, Washington State, Northern Texas, and the Southwest would face more stress due to population growth that is faster than the loss of suitable lands for development. The factors contributing to population stress may differ from place to place. Our population stress concept is useful and innovative for understanding population stress due to land development and can be applied to other regions as well as global research. It can act as a basis towards developing coherent sustainable land use policies. Coordination among local governments and across different levels of governments in the twenty-first century is a must for effective land use planning.

Culture creates genetic structure in the Caucasus: Autosomal, mitochondrial, and Y-chromosomal variation in Daghestan

PubMed Central

Marchani, Elizabeth E; Watkins, W Scott; Bulayeva, Kazima; Harpending, Henry C; Jorde, Lynn B

2008-01-01

Background Near the junction of three major continents, the Caucasus region has been an important thoroughfare for human migration. While the Caucasus Mountains have diverted human traffic to the few lowland regions that provide a gateway from north to south between the Caspian and Black Seas, highland populations have been isolated by their remote geographic location and their practice of patrilocal endogamy. We investigate how these cultural and historical differences between highland and lowland populations have affected patterns of genetic diversity. We test 1) whether the highland practice of patrilocal endogamy has generated sex-specific population relationships, and 2) whether the history of migration and military conquest associated with the lowland populations has left Central Asian genes in the Caucasus, by comparing genetic diversity and pairwise population relationships between Daghestani populations and reference populations throughout Europe and Asia for autosomal, mitochondrial, and Y-chromosomal markers. Results We found that the highland Daghestani populations had contrasting histories for the mitochondrial DNA and Y-chromosome data sets. Y-chromosomal haplogroup diversity was reduced among highland Daghestani populations when compared to other populations and to highland Daghestani mitochondrial DNA haplogroup diversity. Lowland Daghestani populations showed Turkish and Central Asian affinities for both mitochondrial and Y-chromosomal data sets. Autosomal population histories are strongly correlated to the pattern observed for the mitochondrial DNA data set, while the correlation between the mitochondrial DNA and Y-chromosome distance matrices was weak and not significant. Conclusion The reduced Y-chromosomal diversity exhibited by highland Daghestani populations is consistent with genetic drift caused by patrilocal endogamy. Mitochondrial and Y-chromosomal phylogeographic comparisons indicate a common Near Eastern origin of highland populations. Lowland Daghestani populations show varying influence from Near Eastern and Central Asian populations. PMID:18637195

Assessing the effects of hybridization and precipitation on invasive weed demography using strength of selection on vital rates.

PubMed

Teitel, Zachary; Klimowski, Agnieszka; Campbell, Lesley G

2016-12-07

As global climate change transforms average temperature and rainfall, species distributions may meet, increasing the potential for hybridization and altering individual fitness and population growth. Altered rainfall specifically may shift the strength and direction of selection, also manipulating population trajectories. Here, we investigated the role of interspecific hybridization and selection imposed by rainfall on the evolution of weedy life-history in non-hybrid (Raphanus raphanistrum) and hybrid (R. raphanistrum x R. sativus) populations using a life table response experiment. In documenting long-term population dynamics, we determined intrinsic (r) and asymptotic (λ) population growth rates and sensitivities, a measure of selection imposed on demographic rates. Hybrid populations experienced 8.7-10.3 times stronger selection than wild populations for increased seedling survival. Whereas crop populations generally exhibit little dormancy and wild populations often exhibit dormancy, non-hybrid populations experienced 10% stronger selection than hybrid populations for exhibiting seed dormancy. Selection on survival-to-flowering in wild, not hybrid, populations declined marginally with increasing soil moisture. Hybrid populations exhibited greater r, but not λ, than wild populations regardless of moisture environment. In general, fecundity contributed most to differences in λ but fecundity only contributed positively to hybrid λ relative to wild λ when precipitation was altered (either higher or lower than control) and not under control watering conditions. Selection on key demographic traits may not change dramatically in response to rainfall, and hybridization may more strongly influence the demography of these weedy species than rainfall. If hybrid populations can respond to selection for increased dormancy, this may make it more difficult to deplete weed seed banks and increase the persistence of crop genes in weed populations.

Genetic Divergence and Signatures of Natural Selection in Marginal Populations of a Keystone, Long-Lived Conifer, Eastern White Pine (Pinus strobus) from Northern Ontario

PubMed Central

Chhatre, Vikram E.; Rajora, Om P.

2014-01-01

Marginal populations are expected to provide the frontiers for adaptation, evolution and range shifts of plant species under the anticipated climate change conditions. Marginal populations are predicted to show genetic divergence from central populations due to their isolation, and divergent natural selection and genetic drift operating therein. Marginal populations are also expected to have lower genetic diversity and effective population size (N e) and higher genetic differentiation than central populations. We tested these hypotheses using eastern white pine (Pinus strobus) as a model for keystone, long-lived widely-distributed plants. All 614 eastern white pine trees, in a complete census of two populations each of marginal old-growth, central old-growth, and central second-growth, were genotyped at 11 microsatellite loci. The central populations had significantly higher allelic and genotypic diversity, latent genetic potential (LGP) and N e than the marginal populations. However, heterozygosity and fixation index were similar between them. The marginal populations were genetically diverged from the central populations. Model testing suggested predominant north to south gene flow in the study area with curtailed gene flow to northern marginal populations. Signatures of natural selection were detected at three loci in the marginal populations; two showing divergent selection with directional change in allele frequencies, and one balancing selection. Contrary to the general belief, no significant differences were observed in genetic diversity, differentiation, LGP, and N e between old-growth and second-growth populations. Our study provides information on the dynamics of migration, genetic drift and selection in central versus marginal populations of a keystone long-lived plant species and has broad evolutionary, conservation and adaptation significance. PMID:24859159

Updated population metadata for United States historical climatology network stations

USGS Publications Warehouse

Owen, T.W.; Gallo, K.P.

2000-01-01

The United States Historical Climatology Network (HCN) serial temperature dataset is comprised of 1221 high-quality, long-term climate observing stations. The HCN dataset is available in several versions, one of which includes population-based temperature modifications to adjust urban temperatures for the "heat-island" effect. Unfortunately, the decennial population metadata file is not complete as missing values are present for 17.6% of the 12 210 population values associated with the 1221 individual stations during the 1900-90 interval. Retrospective grid-based populations. Within a fixed distance of an HCN station, were estimated through the use of a gridded population density dataset and historically available U.S. Census county data. The grid-based populations for the HCN stations provide values derived from a consistent methodology compared to the current HCN populations that can vary as definitions of the area associated with a city change over time. The use of grid-based populations may minimally be appropriate to augment populations for HCN climate stations that lack any population data, and are recommended when consistent and complete population data are required. The recommended urban temperature adjustments based on the HCN and grid-based methods of estimating station population can be significantly different for individual stations within the HCN dataset.

Evaluation of the genetic structure of sika deer (Cervus nippon) in Japan's Kanto and Tanzawa mountain areas, based on microsatellite markers.

PubMed

Konishi, Sayaka; Hata, Shoko; Matsuda, Sayumi; Arai, Kazushi; Mizoguchi, Yasushi

2017-11-01

The browsing habits of sika deer (Cervus nippon) in Japan have caused serious ecological problems. Appropriate management of sika deer populations requires understanding the different genetic structures of local populations. In the present study, we used 10 microsatellite polymorphisms to explore the genetic structures of sika deer populations (162 individuals) living in the Kanto region. The expected heterozygosity of the Tanzawa mountain range population (Group I) was lower than that of the populations in the Kanto mountain areas (Group II). Our results suggest that moderate gene flow has occurred between the sika deer populations in the Kanto mountain areas (Group II), but not to or from the Tanzawa mountain range population (Group I). Also, genetic structure analysis showed that the Tanzawa population was separated from the other populations. This is probably attributable to a genetic bottleneck that developed in the Tanzawa sika deer population in the 1950s. However, we found that the Tanzawa population has since recovered from the bottleneck situation and now exhibits good genetic diversity. Our results show that it is essential to periodically evaluate the genetic structures of deer populations to develop conservation strategies appropriate to the specific structures of individual populations at any given time. © 2017 Japanese Society of Animal Science.

Locally adaptive, spatially explicit projection of US population for 2030 and 2050.

PubMed

McKee, Jacob J; Rose, Amy N; Bright, Edward A; Huynh, Timmy; Bhaduri, Budhendra L

2015-02-03

Localized adverse events, including natural hazards, epidemiological events, and human conflict, underscore the criticality of quantifying and mapping current population. Building on the spatial interpolation technique previously developed for high-resolution population distribution data (LandScan Global and LandScan USA), we have constructed an empirically informed spatial distribution of projected population of the contiguous United States for 2030 and 2050, depicting one of many possible population futures. Whereas most current large-scale, spatially explicit population projections typically rely on a population gravity model to determine areas of future growth, our projection model departs from these by accounting for multiple components that affect population distribution. Modeled variables, which included land cover, slope, distances to larger cities, and a moving average of current population, were locally adaptive and geographically varying. The resulting weighted surface was used to determine which areas had the greatest likelihood for future population change. Population projections of county level numbers were developed using a modified version of the US Census's projection methodology, with the US Census's official projection as the benchmark. Applications of our model include incorporating multiple various scenario-driven events to produce a range of spatially explicit population futures for suitability modeling, service area planning for governmental agencies, consequence assessment, mitigation planning and implementation, and assessment of spatially vulnerable populations.

Genetic Diversity and Population Parameters of Sea Otters, Enhydra lutris, before Fur Trade Extirpation from 1741–1911

PubMed Central

Larson, Shawn; Jameson, Ron; Etnier, Michael; Jones, Terry; Hall, Roberta

2012-01-01

All existing sea otter, Enhydra lutris, populations have suffered at least one historic population bottleneck stemming from the fur trade extirpations of the eighteenth and nineteenth centuries. We examined genetic variation, gene flow, and population structure at five microsatellite loci in samples from five pre-fur trade populations throughout the sea otter's historical range: California, Oregon, Washington, Alaska, and Russia. We then compared those values to genetic diversity and population structure found within five modern sea otter populations throughout their current range: California, Prince William Sound, Amchitka Island, Southeast Alaska and Washington. We found twice the genetic diversity in the pre-fur trade populations when compared to modern sea otters, a level of diversity that was similar to levels that are found in other mammal populations that have not experienced population bottlenecks. Even with the significant loss in genetic diversity modern sea otters have retained historical structure. There was greater gene flow before extirpation than that found among modern sea otter populations but the difference was not statistically significant. The most dramatic effect of pre fur trade population extirpation was the loss of genetic diversity. For long term conservation of these populations increasing gene flow and the maintenance of remnant genetic diversity should be encouraged. PMID:22403635

Restoration over time and sustainability of Schinus terebinthifolius Raddi.

PubMed

Álvares-Carvalho, S V; Silva-Mann, R; Gois, I B; Melo, M F V; Oliveira, A S; Ferreira, R A; Gomes, L J

2017-05-31

The success of recovery programs on degraded areas is dependent on the genetic material to be used, which should present heterozygosity and genetic diversity in native and recovered populations. This study was carried out to evaluate the model efficiency to enable the recovery of a degraded area of the Lower São Francisco, Sergipe, Brazil. The target species for this study was Schinus terebinthifolius Raddi. Three populations were analyzed, the recovered area, seed-tree source population, and native tree population border established to the recovered area. The random amplified polymorphic DNA (RAPD) markers were used for diversity analysis. Genetic structure was estimated to evaluate the level of genetic variability existent in each population. There was no correlation between the spatial distribution and the genetic distances for all trees of the recovered area. The heterozygosity present in the recovered population was higher than the native tree population. The seed-tree source population presents genetic bottlenecks. Three clusters were suggested (ΔK = 3) with non-genetic structure. High intra-population genetic variability and inter-population differentiation are present. However, gene flow may also introduce potentially adaptive alleles in the populations of the recovered area, and the native population is necessary to ensure the sustainability and maintenance of the populations by allelic exchange.

Vicariance and dispersal across Baja California in disjunct marine fish populations.

PubMed

Bernardi, Giacomo; Findley, Lloyd; Rocha-Olivares, Axayacatl

2003-07-01

Population disjunctions, as a first step toward complete allopatry, present an interesting situation to study incipient speciation. The geological formation of the Baja California Peninsula currently divides 19 species of fish into disjunct populations that are found on its Pacific Coast and in the northern part of the Gulf of California (also called the Sea of Cortez), but are absent from the Cape (Cabo San Lucas) region. We studied the genetic makeup of disjunct populations for 12 of these 19 fish species. Phylogeographic patterns for the 12 species can be separated into two major classes: a first group (eight species) showed reciprocal monophyly and high genetic divergence between disjunct populations. A second group (four species) displayed what appeared to be panmictic populations. Population structure between Pacific Coast populations, across the Punta Eugenia biogeographic boundary, was also evaluated. While dispersal potential (inferred by pelagic larval duration) was a poor predictor of population structure between Gulf of California and Pacific populations, we found that population genetic subdivision along the Pacific Coast at Punta Eugenia was always positively correlated with differentiation between Pacific and Gulf of California populations. Vicariant events, ongoing gene flow, and ecological characteristics played essential roles in shaping the population structures observed in this study.

Human Population: Fundamentals of Growth and Change.

ERIC Educational Resources Information Center

Stauffer, Cheryl Lynn, Ed.

This booklet focuses on eight elements of population dynamics: "Population Growth and Distribution"; "Natural Increase and Future Growth"; "Effect of Migration on Population Growth"; "Three Patterns of Population Change"; "Patterns of World Urbanization"; "The Status of Women";…

The genetic rescue of two bottlenecked South Island robin populations using translocations of inbred donors.

PubMed

Heber, S; Varsani, A; Kuhn, S; Girg, A; Kempenaers, B; Briskie, J

2013-02-07

Populations forced through bottlenecks typically lose genetic variation and exhibit inbreeding depression. 'Genetic rescue' techniques that introduce individuals from outbred populations can be highly effective in reversing the deleterious effects of inbreeding, but have limited application for the majority of endangered species, which survive only in a few bottlenecked populations. We tested the effectiveness of using highly inbred populations as donors to rescue two isolated and bottlenecked populations of the South Island robin (Petroica australis). Reciprocal translocations significantly increased heterozygosity and allelic diversity. Increased genetic diversity was accompanied by increased juvenile survival and recruitment, sperm quality, and immunocompetence of hybrid individuals (crosses between the two populations) compared with inbred control individuals (crosses within each population). Our results confirm that the implementation of 'genetic rescue' using bottlenecked populations as donors provides a way of preserving endangered species and restoring their viability when outbred donor populations no longer exist.

Estimating population sizes for elusive animals: the forest elephants of Kakum National Park, Ghana.

PubMed

Eggert, L S; Eggert, J A; Woodruff, D S

2003-06-01

African forest elephants are difficult to observe in the dense vegetation, and previous studies have relied upon indirect methods to estimate population sizes. Using multilocus genotyping of noninvasively collected samples, we performed a genetic survey of the forest elephant population at Kakum National Park, Ghana. We estimated population size, sex ratio and genetic variability from our data, then combined this information with field observations to divide the population into age groups. Our population size estimate was very close to that obtained using dung counts, the most commonly used indirect method of estimating the population sizes of forest elephant populations. As their habitat is fragmented by expanding human populations, management will be increasingly important to the persistence of forest elephant populations. The data that can be obtained from noninvasively collected samples will help managers plan for the conservation of this keystone species.

Detecting Directional Selection in the Presence of Recent Admixture in African-Americans

PubMed Central

Lohmueller, Kirk E.; Bustamante, Carlos D.; Clark, Andrew G.

2011-01-01

We investigate the performance of tests of neutrality in admixed populations using plausible demographic models for African-American history as well as resequencing data from African and African-American populations. The analysis of both simulated and human resequencing data suggests that recent admixture does not result in an excess of false-positive results for neutrality tests based on the frequency spectrum after accounting for the population growth in the parental African population. Furthermore, when simulating positive selection, Tajima's D, Fu and Li's D, and haplotype homozygosity have lower power to detect population-specific selection using individuals sampled from the admixed population than from the nonadmixed population. Fay and Wu's H test, however, has more power to detect selection using individuals from the admixed population than from the nonadmixed population, especially when the selective sweep ended long ago. Our results have implications for interpreting recent genome-wide scans for positive selection in human populations. PMID:21196524

Genetic and Ecological Outcomes of Inga vera Subsp. affinis (Leguminosae) Tree Plantations in a Fragmented Tropical Landscape

PubMed Central

Cruz Neto, Oswaldo; Aguiar, Antonio V.; Twyford, Alex D.; Neaves, Linda E.; Pennington, R. Toby; Lopes, Ariadna V.

2014-01-01

Planting of native trees for habitat restoration is a widespread practice, but the consequences for the retention and transmission of genetic diversity in planted and natural populations are unclear. Using Inga vera subsp. affinis as a model species, we genotyped five natural and five planted populations in the Atlantic forest of northeastern Brazil at polymorphic microsatellite loci. We studied the breeding system and population structure to test how much genetic diversity is retained in planted relative to natural populations. We then genotyped seedlings from these populations to test whether genetic diversity in planted populations is restored by outcrossing to natural populations of I. vera. The breeding system of natural I. vera populations was confirmed to be highly outcrossing (t = 0.92; FIS = −0.061, P = 0.04), with populations showing weak population substructure (FST = 0.028). Genetic diversity in planted populations was 50% less than that of natural populations (planted: AR = 14.9, HO = 0.865 and natural: AR = 30.8, HO = 0.655). However, seedlings from planted populations showed a 30% higher allelic richness relative to their parents (seedlings AR = 10.5, parents AR = 7.6). Understanding the processes and interactions that shape this system are necessary to provide ecologically sensible goals and successfully restore hyper-fragmented habitats. Future restoration plans for I. vera must consider the genetic diversity of planted populations and the potential for gene flow between natural populations in the landscape, in order to preserve ecological interactions (i.e. pollination), and promote opportunities for outcrossing. PMID:24932729

Genetic and ecological outcomes of Inga vera subsp. affinis (Leguminosae) tree plantations in a fragmented tropical landscape.

PubMed

Cruz Neto, Oswaldo; Aguiar, Antonio V; Twyford, Alex D; Neaves, Linda E; Pennington, R Toby; Lopes, Ariadna V

2014-01-01

Planting of native trees for habitat restoration is a widespread practice, but the consequences for the retention and transmission of genetic diversity in planted and natural populations are unclear. Using Inga vera subsp. affinis as a model species, we genotyped five natural and five planted populations in the Atlantic forest of northeastern Brazil at polymorphic microsatellite loci. We studied the breeding system and population structure to test how much genetic diversity is retained in planted relative to natural populations. We then genotyped seedlings from these populations to test whether genetic diversity in planted populations is restored by outcrossing to natural populations of I. vera. The breeding system of natural I. vera populations was confirmed to be highly outcrossing (t = 0.92; FIS = -0.061, P = 0.04), with populations showing weak population substructure (FST = 0.028). Genetic diversity in planted populations was 50% less than that of natural populations (planted: AR = 14.9, HO = 0.865 and natural: AR = 30.8, HO = 0.655). However, seedlings from planted populations showed a 30% higher allelic richness relative to their parents (seedlings AR = 10.5, parents AR = 7.6). Understanding the processes and interactions that shape this system are necessary to provide ecologically sensible goals and successfully restore hyper-fragmented habitats. Future restoration plans for I. vera must consider the genetic diversity of planted populations and the potential for gene flow between natural populations in the landscape, in order to preserve ecological interactions (i.e. pollination), and promote opportunities for outcrossing.

Using Population Density and Size Class Frequency to Identify Recruitment Limitation and Saturation in Shellfishes

NASA Astrophysics Data System (ADS)

Bennett, B.

2016-02-01

Many fisheries are threatened due to overfishing, changing climate, and anthropogenic activities. Benthic marine organisms can be especially vulnerable to these pressures because of their inability to flee, and some of these organisms comprise the most threatened fisheries. Providing predictive tools to managers is key to reestablishing populations and sustainability in threatened or crashed fisheries. Here we examine the demographics of Cellana spp., culturally and culinarily important intertidal shellfishes in Hawai'i, in populations that are naturally recruitment limited and those that are recruitment saturated. We focus on variation in two demographic parameters: population density and size class frequency. From 2009 to 2015, yearly transect surveys were conducted on four isolated and uninhabited islands within the Papahānaumokuākea Marine National Monument (PMNM), a massive marine protected area. Two islands exhibit classic signs of recruitment limitation with several absent intertidal species and low population densities while two larger islands have a relative abundance of species and high population densities. The population density of C. exarata in the recruitment-saturated populations exhibit much higher variability, than in the recruitment-limited populations, that is driven by a massive recruitment peak in May-June. An inverted age pyramid characterized the recruitment-limited populations, which display a more stable adult-dominated population. The recruitment-saturated populations were characterized by a traditional age pyramid, which exhibit a less stable juvenile-dominated population. These results are being used to model and predict population dynamics in the intensely harvested populations of the main Hawaiian Islands for the purposes of management decision-making.

Living in isolation - population structure, reproduction, and genetic variation of the endangered plant species Dianthus gratianopolitanus (Cheddar pink).

PubMed

Putz, Christina M; Schmid, Christoph; Reisch, Christoph

2015-09-01

The endangered plant species Dianthus gratianopolitanus exhibits a highly fragmented distribution range comprising many isolated populations. Based upon this pattern of distribution, we selected a study region in Switzerland with a lower magnitude of isolation (Swiss Jura) and another study region in Germany with a higher degree of isolation (Franconian Jura). In each region, we chose ten populations to analyze population structure, reproduction, and genetic variation in a comparative approach. Therefore, we determined population density, cushion size, and cushion density to analyze population structure, investigated reproductive traits, including number of flowers, capsules, and germination rate, and analyzed amplified fragment length polymorphisms to study genetic variation. Population and cushion density were credibly higher in German than in Swiss populations, whereas reproductive traits and genetic variation within populations were similar in both study regions. However, genetic variation among populations and isolation by distance were stronger in Germany than in Switzerland. Generally, cushion size and density as well as flower and capsule production increased with population size and density, whereas genetic variation decreased with population density. In contrast to our assumptions, we observed denser populations and cushions in the region with the higher magnitude of isolation, whereas reproductive traits and genetic variation within populations were comparable in both regions. This corroborates the assumption that stronger isolation must not necessarily result in the loss of fitness and genetic variation. Furthermore, it supports our conclusion that the protection of strongly isolated populations contributes essentially to the conservation of a species' full evolutionary potential.

Genetic analysis of haplotype data for 23 Y-chromosome short tandem repeat loci in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina

PubMed Central

Dogan, Serkan; Primorac, Dragan; Marjanović, Damir

2014-01-01

Aim To explore the distribution and polymorphisms of 23 short tandem repeat (STR) loci on the Y chromosome in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina and to investigate its genetic relationships with the homeland Turkish population and neighboring populations. Methods This study included 100 healthy unrelated male individuals from the Turkish population living in Sarajevo. Buccal swab samples were collected as a DNA source. Genomic DNA was extracted using the salting out method and amplification was performed using PowerPlex Y 23 amplification kit. The studied population was compared to other populations using pairwise genetic distances, which were represented with a multi-dimensional scaling plot. Results Haplotype and allele frequencies of the sample population were calculated and the results showed that all 100 samples had unique haplotypes. The most polymorphic locus was DYS458, and the least polymorphic DYS391. The observed haplotype diversity was 1.0000 ± 0.0014, with a discrimination capacity of 1.00 and the match probability of 0.01. Rst values showed that our sample population was closely related in both dimensions to the Lebanese and Iraqi populations, while it was more distant from Bosnian, Croatian, and Macedonian populations. Conclusion Turkish population residing in Sarajevo could be observed as a representative Turkish population, since our results were consistent with those previously published for the homeland Turkish population. Also, this study once again proved that geographically close populations were genetically more related to each other. PMID:25358886

Natural Selection and Neutral Evolution Jointly Drive Population Divergence between Alpine and Lowland Ecotypes of the Allopolyploid Plant Anemone multifida (Ranunculaceae)

PubMed Central

McEwen, Jamie R.; Vamosi, Jana C.; Rogers, Sean M.

2013-01-01

Population differentiation can be driven in large part by natural selection, but selectively neutral evolution can play a prominent role in shaping patters of population divergence. The decomposition of the evolutionary history of populations into the relative effects of natural selection and selectively neutral evolution enables an understanding of the causes of population divergence and adaptation. In this study, we examined heterogeneous genomic divergence between alpine and lowland ecotypes of the allopolyploid plant, Anemone multifida. Using peak height and dominant AFLP data, we quantified population differentiation at non-outlier (neutral) and outlier loci to determine the potential contribution of natural selection and selectively neutral evolution to population divergence. We found 13 candidate loci, corresponding to 2.7% of loci, with signatures of divergent natural selection between alpine and lowland populations and between alpine populations (Fst  = 0.074–0.445 at outlier loci), but neutral population differentiation was also evident between alpine populations (FST  = 0.041–0.095 at neutral loci). By examining population structure at both neutral and outlier loci, we determined that the combined effects of selection and neutral evolution are associated with the divergence of alpine populations, which may be linked to extreme abiotic conditions and isolation between alpine sites. The presence of outlier levels of genetic variation in structured populations underscores the importance of separately analyzing neutral and outlier loci to infer the relative role of divergent natural selection and neutral evolution in population divergence. PMID:23874801

Comparison of sexual compatibility in crosses between the southern and northern populations of the cabbage beetle Colaphellus bowringi.

PubMed

Liu, Xing-Ping; Tu, Xiao-Yun; He, Hai-Min; Chen, Chao; Xue, Fang-Sen

2014-12-01

It is widely accepted that the genetic divergence and reproductive incompatibility between closely related species and/or populations is often viewed as an important step toward speciation. In this study, sexual compatibility in crosses between the southern XS population and the northern TA population of the polyandrous cabbage beetle Colaphellus bowringi was investigated by testing their mating preferences, mating latency, copulation duration, and reproductive performances of post-mating. In choice mating experiments, the percentages of matings were significantly higher in intra-population crosses than in inter-population crosses. Both isolation index (I) and index of pair sexual isolation (IPSI ) indicated partial mating incompatibility or assortative mating in crosses between the two different geographical populations. In single pair mating experiments, XS females in inter-population crosses mated significantly later and copulated significantly shorter than those in intra-population crosses. However, TA females in inter-population crosses mated significantly earlier and copulated longer than those in intra-population crosses, suggesting that larger XS males may enhance heterotypic mating. The lifetime fecundity was highest in XS homotypic matings, lowest in TA homotypic matings, and intermediate in heterotypic matings between their parents. The inter-population crosses resulted in significantly lower egg hatching rate and shorter female longevity than intra-population crosses. These results demonstrated that there exist some incompatibilities in premating, postmating-prezygotic, and postzygotic stages between the southern XS population and northern TA population of the cabbage beetle Colaphellus bowringi. © 2013 Institute of Zoology, Chinese Academy of Sciences.

Patterns of ancestry and genetic diversity in reintroduced populations of the slimy sculpin: Implications for conservation

USGS Publications Warehouse

Huff, David D.; Miller, Loren M.; Vondracek, Bruce C.

2010-01-01

Reintroductions are a common approach for preserving intraspecific biodiversity in fragmented landscapes. However, they may exacerbate the reduction in genetic diversity initially caused by population fragmentation because the effective population size of reintroduced populations is often smaller and reintroduced populations also tend to be more geographically isolated than native populations. Mixing genetically divergent sources for reintroduction purposes is a practice intended to increase genetic diversity. We documented the outcome of reintroductions from three mixed sources on the ancestral composition and genetic variation of a North American fish, the slimy sculpin (Cottus cognatus). We used microsatellite markers to evaluate allelic richness and heterozygosity in the reintroduced populations relative to computer simulated expectations. Sculpins in reintroduced populations exhibited higher levels of heterozygosity and allelic richness than any single source, but only slightly higher than the single most genetically diverse source population. Simulations intended to mimic an ideal scenario for maximizing genetic variation in the reintroduced populations also predicted increases, but they were only moderately greater than the most variable source population. We found that a single source contributed more than the other two sources at most reintroduction sites. We urge caution when choosing whether to mix source populations in reintroduction programs. Genetic characteristics of candidate source populations should be evaluated prior to reintroduction if feasible. When combined with knowledge of the degree of genetic distinction among sources, simulations may allow the genetic diversity benefits of mixing populations to be weighed against the risks of outbreeding depression in reintroduced and nearby populations.

Patterns of ancestry and genetic diversity in reintroduced populations of the slimy sculpin: Implications for conservation

USGS Publications Warehouse

Huff, D.D.; Miller, L.M.; Vondracek, B.

2010-01-01

Reintroductions are a common approach for preserving intraspecific biodiversity in fragmented landscapes. However, they may exacerbate the reduction in genetic diversity initially caused by population fragmentation because the effective population size of reintroduced populations is often smaller and reintroduced populations also tend to be more geographically isolated than native populations. Mixing genetically divergent sources for reintroduction purposes is a practice intended to increase genetic diversity. We documented the outcome of reintroductions from three mixed sources on the ancestral composition and genetic variation of a North American fish, the slimy sculpin (Cottus cognatus). We used microsatellite markers to evaluate allelic richness and heterozygosity in the reintroduced populations relative to computer simulated expectations. Sculpins in reintroduced populations exhibited higher levels of heterozygosity and allelic richness than any single source, but only slightly higher than the single most genetically diverse source population. Simulations intended to mimic an ideal scenario for maximizing genetic variation in the reintroduced populations also predicted increases, but they were only moderately greater than the most variable source population. We found that a single source contributed more than the other two sources at most reintroduction sites. We urge caution when choosing whether to mix source populations in reintroduction programs. Genetic characteristics of candidate source populations should be evaluated prior to reintroduction if feasible. When combined with knowledge of the degree of genetic distinction among sources, simulations may allow the genetic diversity benefits of mixing populations to be weighed against the risks of outbreeding depression in reintroduced and nearby populations. ?? 2010 US Government.

Marshes as "Mountain Tops": Genetic Analyses of the Critically Endangered São Paulo Marsh Antwren (Aves: Thamnophilidae).

PubMed

de Camargo, Crisley; Gibbs, H Lisle; Costa, Mariellen C; Del-Rio, Glaucia; Silveira, Luís F; Wasko, Adriane P; Francisco, Mercival R

2015-01-01

Small populations of endangered species can be impacted by genetic processes such as drift and inbreeding that reduce population viability. As such, conservation genetic analyses that assess population levels of genetic variation and levels of gene flow can provide important information for managing threatened species. The São Paulo Marsh Antwren (Formicivora paludicola) is a recently-described and critically endangered bird from São Paulo State (Brazil) whose total estimated population is around 250-300 individuals, distributed in only 15 isolated marshes around São Paulo metropolitan region. We used microsatellite DNA markers to estimate the population genetic characteristics of the three largest remaining populations of this species all within 60 km of each other. We detected a high and significant genetic structure between all populations (overall FST = 0.103) which is comparable to the highest levels of differentiation ever documented for birds, (e.g., endangered birds found in isolated populations on the tops of African mountains), but also evidence for first-generation immigrants, likely from small local unsampled populations. Effective population sizes were small (between 28.8-99.9 individuals) yet there are high levels of genetic variability within populations and no evidence for inbreeding. Conservation implications of this work are that the high levels of genetic structure suggests that translocations between populations need to be carefully considered in light of possible local adaptation and that remaining populations of these birds should be managed as conservation units that contain both main populations studied here but also small outlying populations which may be a source of immigrants.

Genetic Divergence Disclosing a Rapid Prehistorical Dispersion of Native Americans in Central and South America

PubMed Central

He, Yungang; Wang, Wei R.; Li, Ran; Wang, Sijia; Jin, Li

2012-01-01

An accurate estimate of the divergence time between Native Americans is important for understanding the initial entry and early dispersion of human beings in the New World. Current methods for estimating the genetic divergence time of populations could seriously depart from a linear relationship with the true divergence for multiple populations of a different population size and significant population expansion. Here, to address this problem, we propose a novel measure to estimate the genetic divergence time of populations. Computer simulation revealed that the new measure maintained an excellent linear correlation with the population divergence time in complicated multi-population scenarios with population expansion. Utilizing the new measure and microsatellite data of 21 Native American populations, we investigated the genetic divergences of the Native American populations. The results indicated that genetic divergences between North American populations are greater than that between Central and South American populations. None of the divergences, however, were large enough to constitute convincing evidence supporting the two-wave or multi-wave migration model for the initial entry of human beings into America. The genetic affinity of the Native American populations was further explored using Neighbor-Net and the genetic divergences suggested that these populations could be categorized into four genetic groups living in four different ecologic zones. The divergence of the population groups suggests that the early dispersion of human beings in America was a multi-step procedure. Further, the divergences suggest the rapid dispersion of Native Americans in Central and South Americas after a long standstill period in North America. PMID:22970308

Population Education Country Programmes.

ERIC Educational Resources Information Center

Population Education in Asia and the Pacific Newsletter, 1983

1983-01-01

Describes population programs in Afghanistan (nonformal, population education literacy program), India (problems in planning/managing population education in higher education), Indonesia (training for secondary/out-of-school inspectors), and Pakistan (integration of population education into school curricula). Programs in China, Korea, Vietnam,…

WHAT IS A POPULATION?

EPA Science Inventory

The word "population" has several meanings, a situation that can lead to confusion in risk assessments. A management goal "to protect wildlife populations," for example, might relate to populations as defined by population biologists, or it might mean simply to protect animals in...

The New Population Debate: Two Views on Population Growth and Economic Development. Population Trends and Public Policy, Number 7.

ERIC Educational Resources Information Center

King, Timothy; Kelley, Allen C.

Articles representing two views on the issue of rapid population growth and economic development are presented. Although the authors present different perspectives, they agree on many of the fundamentals. For example, both reject alarmism about impending "population explosions" and the use of population as a scapegoat for all Third World…

America's Families and Living Arrangements: 2003. Population Characteristics. Current Population Reports. P20-553

ERIC Educational Resources Information Center

Fields, Jason

2004-01-01

The data in this report is from the Annual Social and Economic Supplement (ASEC) to the 2003 Current Population Survey (CPS). The population represented (the population universe) in the ASEC is the civilian non institutionalized population living in the United States. Members of the Armed Forces living off post or with their families on post are…

Population Education in the United States: A Report to the Commission on Population Growth and the American Future.

ERIC Educational Resources Information Center

Viederman, Stephen

Population education is a planned, integrated, and sequential approach to population learning. It is defined as the process by which the student investigates the nature and meaning of population processes and characteristics, the causes of population changes, and the consequences of these for himself, his family, his society, and the world. Its…

Bight of Benin: a Maternal Perspective of Four Beninese Populations and their Genetic Implications on the American Populations of African Ancestry.

PubMed

Primativo, Giuseppina; Ottoni, Claudio; Biondi, Gianfranco; Serafino, Sara; Martínez-Labarga, Cristina; Larmuseau, Maarten H D; Scardi, Michele; Decorte, Ronny; Rickards, Olga

2017-03-01

The understanding of the first movements of the ancestral populations within the African continent is still unclear, particularly in West Africa, due to several factors that have shaped the African genetic pool across time. To improve the genetic representativeness of the Beninese population and to better understand the patterns of human settlement inside West Africa and the dynamics of peopling of the Democratic Republic of Benin, we analyzed the maternal genetic variation of 193 Beninese individuals belonging to Bariba, Berba, Dendi, and Fon populations. Results support the oral traditions indicating that the western neighbouring populations have been the ancestors of the first Beninese populations, and the extant genetic structure of the Beninese populations is most likely the result of admixture between populations from neighbouring countries and native people. The present findings highlight how the Beninese populations contributed to the gene pool of the extant populations of some American populations of African ancestry. This strengthens the hypothesis that the Bight of Benin was not only an assembly point for the slave trade during the Trans-Atlantic Slave Trade but also an important slave trapping area. © 2017 John Wiley & Sons Ltd/University College London.

Size and age structure of anadromous and landlocked populations of Rainbow Smelt

USGS Publications Warehouse

O'Malley, Andrew; Enterline, Claire; Zydlewski, Joseph D.

2017-01-01

Rainbow Smelt Osmerus mordax are widely distributed in both anadromous and landlocked populations throughout northeastern North America; abundance, size at age, and maximum size vary widely among populations and life histories. In the present study, size at age, von Bertalanffy growth parameters, population age distributions, and precision and bias in age assessment based on scales and sectioned otoliths were compared between ecotypes and among populations of Rainbow Smelt. To compare the ecotypes, we collected spawning adults from four anadromous and three landlocked populations in Maine during spring 2014. A significant bias was identified in only one of four scale comparisons but in four of seven otolith comparisons; however, a comparable level of precision was indicated. Anadromous populations had larger and more variable size at age and von Bertalanffy growth parameters than landlocked fish. Populations were composed of ages 1–4; six populations were dominated by age-2 or age-3 individuals, and one population was dominated by age-1 fish. These data suggest the presence of considerable plasticity among populations. A latitudinal gradient was observed in the anadromous Rainbow Smelt, which may show signs of population stress at the southern extent of their distribution.

Characterising private and shared signatures of positive selection in 37 Asian populations.

PubMed

Liu, Xuanyao; Lu, Dongsheng; Saw, Woei-Yuh; Shaw, Philip J; Wangkumhang, Pongsakorn; Ngamphiw, Chumpol; Fucharoen, Suthat; Lert-Itthiporn, Worachart; Chin-Inmanu, Kwanrutai; Chau, Tran Nguyen Bich; Anders, Katie; Kasturiratne, Anuradhani; de Silva, H Janaka; Katsuya, Tomohiro; Kimura, Ryosuke; Nabika, Toru; Ohkubo, Takayoshi; Tabara, Yasuharu; Takeuchi, Fumihiko; Yamamoto, Ken; Yokota, Mitsuhiro; Mamatyusupu, Dolikun; Yang, Wenjun; Chung, Yeun-Jun; Jin, Li; Hoh, Boon-Peng; Wickremasinghe, Ananda R; Ong, RickTwee-Hee; Khor, Chiea-Chuen; Dunstan, Sarah J; Simmons, Cameron; Tongsima, Sissades; Suriyaphol, Prapat; Kato, Norihiro; Xu, Shuhua; Teo, Yik-Ying

2017-04-01

The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major groups based on their genographic information. By applying a highly sensitive algorithm haploPS to locate genomic signatures of positive selection, 140 distinct genomic regions exhibiting evidence of positive selection in at least one population were identified. We examined the extent of signal sharing for regions that were selected in multiple populations and observed that populations clustered in a similar fashion to that of how the ancestry clades were phylogenetically defined. In particular, populations predominantly located in South Asia underwent considerably different adaptation as compared with populations from the other geographical regions. Signatures of positive selection present in multiple geographical regions were predicted to be older and have emerged prior to the separation of the populations in the different regions. In contrast, selection signals present in a single population group tended to be of lower frequencies and thus can be attributed to recent evolutionary events.

Profiling the mobile-only population in Australia: insights from the Australian National Health Survey.

PubMed

Baffour, Bernard; Haynes, Michele; Dinsdale, Shane; Western, Mark; Pennay, Darren

2016-10-01

The Australian population that relies on mobile phones exclusively has increased from 5% in 2005 to 29% in 2014. Failing to include this mobile-only population leads to a potential bias in estimates from landline-based telephone surveys. This paper considers the impacts on selected health prevalence estimates with and without the mobile-only population. Using data from the Australian Health Survey - which, for the first time, included a question on telephone status - we examined demographic, geographic and health differences between the landline-accessible and mobile-only population. These groups were also compared to the full population, controlling for the sampling design and differential non-response patterns in the observed sample through weighting and benchmarking. The landline-accessible population differs from the mobile-only population for selected health measures resulting in biased prevalence estimates for smoking, alcohol risk and private health insurance coverage in the full population. The differences remain even after adjusting for age and gender. Using landline telephones only for conducting population health surveys will have an impact on prevalence rate estimates of health risk factors due to the differing profiles of the mobile-only population from the landline-accessible population. © 2016 Public Health Association of Australia.

Applying Thiessen Polygon Catchment Areas and Gridded Population Weights to Estimate Conflict-Driven Population Changes in South Sudan

NASA Astrophysics Data System (ADS)

Jordan, L.

2017-10-01

Recent violence in South Sudan produced significant levels of conflict-driven migration undermining the accuracy and utility of both national and local level population forecasts commonly used in demographic estimates, public health metrics and food security proxies. This article explores the use of Thiessen Polygons and population grids (Gridded Population of the World, WorldPop and LandScan) as weights for estimating the catchment areas for settlement locations that serve large populations of internally displaced persons (IDP), in order to estimate the county-level in- and out-migration attributable to conflict-driven displacement between 2014-2015. Acknowledging IDP totals improves internal population estimates presented by global population databases. Unlike other forecasts, which produce spatially uniform increases in population, accounting for displaced population reveals that 15 percent of counties (n = 12) increased in population over 20 percent, and 30 percent of counties (n = 24) experienced zero or declining population growth, due to internal displacement and refugee out-migration. Adopting Thiessen Polygon catchment zones for internal migration estimation can be applied to other areas with United Nations IDP settlement data, such as Yemen, Somalia, and Nigeria.

Characterising private and shared signatures of positive selection in 37 Asian populations

PubMed Central

Liu, Xuanyao; Lu, Dongsheng; Saw, Woei-Yuh; Shaw, Philip J; Wangkumhang, Pongsakorn; Ngamphiw, Chumpol; Fucharoen, Suthat; Lert-itthiporn, Worachart; Chin-inmanu, Kwanrutai; Chau, Tran Nguyen Bich; Anders, Katie; Kasturiratne, Anuradhani; de Silva, H Janaka; Katsuya, Tomohiro; Kimura, Ryosuke; Nabika, Toru; Ohkubo, Takayoshi; Tabara, Yasuharu; Takeuchi, Fumihiko; Yamamoto, Ken; Yokota, Mitsuhiro; Mamatyusupu, Dolikun; Yang, Wenjun; Chung, Yeun-Jun; Jin, Li; Hoh, Boon-Peng; Wickremasinghe, Ananda R; Ong, RickTwee-Hee; Khor, Chiea-Chuen; Dunstan, Sarah J; Simmons, Cameron; Tongsima, Sissades; Suriyaphol, Prapat; Kato, Norihiro; Xu, Shuhua; Teo, Yik-Ying

2017-01-01

The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major groups based on their genographic information. By applying a highly sensitive algorithm haploPS to locate genomic signatures of positive selection, 140 distinct genomic regions exhibiting evidence of positive selection in at least one population were identified. We examined the extent of signal sharing for regions that were selected in multiple populations and observed that populations clustered in a similar fashion to that of how the ancestry clades were phylogenetically defined. In particular, populations predominantly located in South Asia underwent considerably different adaptation as compared with populations from the other geographical regions. Signatures of positive selection present in multiple geographical regions were predicted to be older and have emerged prior to the separation of the populations in the different regions. In contrast, selection signals present in a single population group tended to be of lower frequencies and thus can be attributed to recent evolutionary events. PMID:28098149

Comparative phylogeny and historical perspectives on population genetics of the Pacific hawksbill (Eretmochelys imbricata) and green turtles (Chelonia mydas), inferred from feeding populations in the Yaeyama Islands, Japan.

PubMed

Nishizawa, Hideaki; Okuyama, Junichi; Kobayashi, Masato; Abe, Osamu; Arai, Nobuaki

2010-01-01

Mitochondrial DNA sequence polymorphisms and patterns of genetic diversity represent the genealogy and relative impacts of historical, geographic, and demographic events on populations. In this study, historical patterns of population dynamics and differentiation in hawksbill (Eretmochelys imbricata) and green turtles (Chelonia mydas) in the Pacific were estimated from feeding populations in the Yaeyama Islands, Japan. Phylogenetic relationships of the haplotypes indicated that hawksbill and green turtles in the Pacific probably underwent very similar patterns and processes of population dynamics over the last million years, with population subdivision during the early Pleistocene and population expansion after the last glacial maximum. These significant contemporary historical events were suggested to have been caused by climatic and sea-level fluctuations. On the other hand, comparing our results to long-term population dynamics in the Atlantic, population subdivisions during the early Pleistocene were specific to Pacific hawksbill and green turtles. Therefore, regional differences in historical population dynamics are suggested. Despite limited sampling locations, these results are the first step in estimating the historical trends in Pacific sea turtles by using phylogenetics and population genetics.

Revisiting evolutionary dead ends in sockeye salmon ( Oncorhynchus nerka) life history

USGS Publications Warehouse

Pavey, S.A.; Hamon, T.R.; Nielsen, J.L.

2007-01-01

This study challenges recent hypotheses about sockeye salmon (Oncorhynchus nerka) colonization based on life history and broadens the pathways that investigators should consider when studying sockeye colonization of novel habitats. Most sockeye populations exhibit lake-type life histories. Riverine populations are thought to be more likely to stray from their natal stream to spawn and therefore colonize new habitat. We examined genetic relationships among five geographically proximate sockeye populations from the Aniakchak region of the Alaska Peninsula, Alaska. Specifically, we sought to determine if the genetic population structure was consistent with the hypothesis that a riverine population colonized a recently available upriver volcanic caldera lake, and whether recent volcanism led to genetic bottlenecks in these sockeye populations. Heterozygosity and allelic richness were not higher in the riverine population. Patterns of genetic divergence suggested that the geographically proximate riverine sockeye population did not colonize the lake; the caldera populations were more genetically divergent from the downstream riverine population (FST  =  0.047) than a lake-type population in a different drainage (FST  =  0.018). Our results did not suggest the presence of genetic bottlenecks in the caldera populations.

On the number of New World founders: a population genetic portrait of the peopling of the Americas.

PubMed

Hey, Jody

2005-06-01

The founding of New World populations by Asian peoples is the focus of considerable archaeological and genetic research, and there persist important questions on when and how these events occurred. Genetic data offer great potential for the study of human population history, but there are significant challenges in discerning distinct demographic processes. A new method for the study of diverging populations was applied to questions on the founding and history of Amerind-speaking Native American populations. The model permits estimation of founding population sizes, changes in population size, time of population formation, and gene flow. Analyses of data from nine loci are consistent with the general portrait that has emerged from archaeological and other kinds of evidence. The estimated effective size of the founding population for the New World is fewer than 80 individuals, approximately 1% of the effective size of the estimated ancestral Asian population. By adding a splitting parameter to population divergence models it becomes possible to develop detailed portraits of human demographic history. Analyses of Asian and New World data support a model of a recent founding of the New World by a population of quite small effective size.

Diversity and divergence among the tribal populations of India.

PubMed

Watkins, W S; Prasad, B V R; Naidu, J M; Rao, B B; Bhanu, B A; Ramachandran, B; Das, P K; Gai, P B; Reddy, P C; Reddy, P G; Sethuraman, M; Bamshad, M J; Jorde, L B

2005-11-01

Tribal populations of the Indian subcontinent have been of longstanding interest to anthropologists and human geneticists. To investigate the relationship of Indian tribes to Indian castes and continental populations, we analyzed 45 unlinked autosomal STR loci in 9 tribal groups, 8 castes, and 18 populations from Africa, Europe and East Asia. South Indian tribal populations demonstrate low within-population heterozygosity (range: 0.54 - 0.69), while tribal populations sampled further north and east have higher heterozygosity (range: 0.69 - 0.74). Genetic distance estimates show that tribal Indians are more closely related to caste Indians than to other major groups. Between-tribe differentiation is high and exceeds that for eight sub-Saharan African populations (4.8% vs. 3.7%). Telugu-speaking populations are less differentiated than non-Telugu speakers (F(ST): 0.029 vs. 0.079), but geographic distance was not predictive of genetic affinity between tribes. South Indian tribes show significant population structure, and individuals can be clustered statistically into groups that correspond with their tribal affiliation. These results are consistent with high levels of genetic drift and isolation in Indian tribal populations, particularly those of South India, and they imply that these populations may be potential candidates for linkage disequilibrium and association mapping.

Epidemiological tracking and population assignment of the non-clonal bacterium, Burkholderia pseudomallei.

PubMed

Dale, Julia; Price, Erin P; Hornstra, Heidie; Busch, Joseph D; Mayo, Mark; Godoy, Daniel; Wuthiekanun, Vanaporn; Baker, Anthony; Foster, Jeffrey T; Wagner, David M; Tuanyok, Apichai; Warner, Jeffrey; Spratt, Brian G; Peacock, Sharon J; Currie, Bart J; Keim, Paul; Pearson, Talima

2011-12-01

Rapid assignment of bacterial pathogens into predefined populations is an important first step for epidemiological tracking. For clonal species, a single allele can theoretically define a population. For non-clonal species such as Burkholderia pseudomallei, however, shared allelic states between distantly related isolates make it more difficult to identify population defining characteristics. Two distinct B. pseudomallei populations have been previously identified using multilocus sequence typing (MLST). These populations correlate with the major foci of endemicity (Australia and Southeast Asia). Here, we use multiple Bayesian approaches to evaluate the compositional robustness of these populations, and provide assignment results for MLST sequence types (STs). Our goal was to provide a reference for assigning STs to an established population without the need for further computational analyses. We also provide allele frequency results for each population to enable estimation of population assignment even when novel STs are discovered. The ability for humans and potentially contaminated goods to move rapidly across the globe complicates the task of identifying the source of an infection or outbreak. Population genetic dynamics of B. pseudomallei are particularly complicated relative to other bacterial pathogens, but the work here provides the ability for broad scale population assignment. As there is currently no independent empirical measure of successful population assignment, we provide comprehensive analytical details of our comparisons to enable the reader to evaluate the robustness of population designations and assignments as they pertain to individual research questions. Finer scale subdivision and verification of current population compositions will likely be possible with genotyping data that more comprehensively samples the genome. The approach used here may be valuable for other non-clonal pathogens that lack simple group-defining genetic characteristics and provides a rapid reference for epidemiologists wishing to track the origin of infection without the need to compile population data and learn population assignment algorithms.

The Population Growth and Carrying Capacity in Semarang City

NASA Astrophysics Data System (ADS)

Hariyanto; Hadi, Sudharto P.; Buchori, Imam

2018-02-01

Population growth and development of city activities take some lands to carry them. As a result, land use competition happens among persons, society or sector. Land necessity for settlement, industry, or sector has taken over farm land, therefore farm land has been converted intensively and massively. Chronologically, population growth will cause land necessity increase. Unproductive land, especially farm land will be converted. Furthermore, farm land conversion will cause carrying capacity change. Carrying capacity has certain bio capacity. With the population growth, it will increase resource consumption; on the other side, farm land conversion will decrease carrying capacity. The objective of the study is to know about the influence of population growth towards carrying capacity (bio capacity) in Semarang city. Land consumption per capita is indeed influenced by city population, the higher the population is, the lower the land consumption per capita. With the population growth, it will influence carrying capacity. Carrying capacity here is the ratio of area to population. Analytical descriptive method is applied in the study with all sub-districts in Semarang city as the analysis unit. Population here is sub-district area and population per sub-district in Semarang city. Population growth data period is from 2000 until 2015. Main variables of the study are area per sub-district, population, population growth, carrying capacity. Result of the study shows significant influence of carrying capacity decrease, especially some outskirts in Semarang city. This condition happens because the outskirts in Semarang city tend to have dense population growth. Range of carrying capacity in Semarang city is from 0,007 to 0,117 of 0 to 1. Almost all sub-districts in Semarang city show miserable condition, except Mijen and Tugu. The conclusion of the study is that population will decrease carrying capacity. Therefore, the government should control population growth by paying attention to its distribution.

Genetic structure of coexisting wild and managed agave populations: implications for the evolution of plants under domestication

PubMed Central

Figueredo, Carmen Julia; Casas, Alejandro; González-Rodríguez, Antonio; Nassar, Jafet M.; Colunga-GarcíaMarín, Patricia; Rocha-Ramírez, Víctor

2015-01-01

Domestication is a continuous evolutionary process guided by humans. This process leads to divergence in characteristics such as behaviour, morphology or genetics, between wild and managed populations. Agaves have been important resources for Mesoamerican peoples since prehistory. Some species are domesticated and others vary in degree of domestication. Agave inaequidens Koch is used in central Mexico to produce mescal, and a management gradient from gathered wild and silvicultural populations, as well as cultivated plantations, has been documented. Significant morphological differences were reported among wild and managed populations, and a high phenotypic variation in cultivated populations composed of plants from different populations. We evaluated levels of genetic diversity and structure associated with management, hypothesizing that high morphological variation would be accompanied by high genetic diversity in populations with high gene flow and low genetic structure among managed and unmanaged populations. Wild, silvicultural and cultivated populations were studied, collecting tissue of 19–30 plants per population. Through 10 nuclear microsatellite loci, we compared population genetic parameters. We analysed partition of variation associated with management categories to estimate gene flow among populations. Agave inaequidens exhibits high levels of genetic diversity (He = 0.707) and moderate genetic structure (FST = 0.112). No differences were found in levels of genetic diversity among wild (He = 0.704), silviculturally managed (He = 0.733) and cultivated (He = 0.698) populations. Bayesian analysis indicated that five genetic clusters best fit the data, with genetic groups corresponding to habitats where populations grow rather than to management. Migration rates ranged from zero between two populations to markedly high among others (M = 0.73–35.25). Natural mechanisms of gene flow and the dynamic management of agave propagules among populations favour gene flow and the maintenance of high levels of variation within all populations. The slight differentiation associated with management indicates that domestication is in an incipient stage. PMID:26433707

Managing the Cayo Santiago rhesus macaque population: The role of density.

PubMed

Hernandez-Pacheco, Raisa; Delgado, Diana L; Rawlins, Richard G; Kessler, Matthew J; Ruiz-Lambides, Angelina V; Maldonado, Elizabeth; Sabat, Alberto M

2016-01-01

Cayo Santiago is the oldest continuously operating free-ranging rhesus monkey colony in the world. Population control of this colony has historically been carried out by periodic live capture and removal of animals. However, the effect of such a strategy on the size, growth rate, age structure, and sex ratio of the population has not been analyzed. This study reviews past removal data and uses a population projection model to simulate the effects of different removal schemes based on Cayo Santiago demographic data from 2000-2012. The model incorporates negative density-dependence in female fertility, as well as male and female survival rates, to determine the population-level effects of selective removal by age and sex. Modeling revealed that removal of sexually immature individuals has negligible effects on the population dynamics explaining why with an initial population of 1309 in 2000 and annual removals of immature monkeys a mean annual population growth rate of 12% and a final population size of ∼1,435 individuals by 2012 (∼0.009 animal/m(2) ) was observed. With no removals, the population is expected to exhibit dampened oscillations until reaching equilibrium at ∼1,690 individuals (∼0.0111 animal/m(2) ) in 2,100. In contrast, removal of adult females (≥4 yrs) would significantly reduce the population size, but would also promote an increase in population growth rate due to density feedback. A maximum annual production of 275 births is expected when 550 adult females are present in the population. Sensitivity analyses showed that removing females, in contrast to controlling their fertility through invasive treatments would contribute the most to changes in population growth rate. Given the density compensation on fertility, stabilizing the population would require removing ∼80% of the current population of adult females. This study highlights the importance of addressing the population-level density effects, as well as sensitivity analyses, to optimize management strategies. © 2016 Wiley Periodicals, Inc.

Protecting vulnerable populations from pandemic influenza in the United States: a strategic imperative.

PubMed

Hutchins, Sonja S; Truman, Benedict I; Merlin, Toby L; Redd, Stephen C

2009-10-01

Protecting vulnerable populations from pandemic influenza is a strategic imperative. The US national strategy for pandemic influenza preparedness and response assigns roles to governments, businesses, civic and community-based organizations, individuals, and families. Because influenza is highly contagious, inadequate preparedness or untimely response in vulnerable populations increases the risk of infection for the general population. Recent public health emergencies have reinforced the importance of preparedness and the challenges of effective response among vulnerable populations. We explore definitions and determinants of vulnerable, at-risk, and special populations and highlight approaches for ensuring that pandemic influenza preparedness includes these populations and enables them to respond appropriately. We also provide an overview of population-specific and cross-cutting articles in this theme issue on influenza preparedness for vulnerable populations.

Protecting Vulnerable Populations From Pandemic Influenza in the United States: A Strategic Imperative

PubMed Central

Truman, Benedict I.; Merlin, Toby L.; Redd, Stephen C.

2009-01-01

Protecting vulnerable populations from pandemic influenza is a strategic imperative. The US national strategy for pandemic influenza preparedness and response assigns roles to governments, businesses, civic and community-based organizations, individuals, and families. Because influenza is highly contagious, inadequate preparedness or untimely response in vulnerable populations increases the risk of infection for the general population. Recent public health emergencies have reinforced the importance of preparedness and the challenges of effective response among vulnerable populations. We explore definitions and determinants of vulnerable, at-risk, and special populations and highlight approaches for ensuring that pandemic influenza preparedness includes these populations and enables them to respond appropriately. We also provide an overview of population-specific and cross-cutting articles in this theme issue on influenza preparedness for vulnerable populations. PMID:19797737

Interactions between demography and environmental effects are important determinants of population dynamics

PubMed Central

Gamelon, Marlène; Grøtan, Vidar; Nilsson, Anna L. K.; Engen, Steinar; Hurrell, James W.; Jerstad, Kurt; Phillips, Adam S.; Røstad, Ole W.; Slagsvold, Tore; Walseng, Bjørn; Stenseth, Nils C.; Sæther, Bernt-Erik

2017-01-01

Climate change will affect the population dynamics of many species, yet the consequences for the long-term persistence of populations are poorly understood. A major reason for this is that density-dependent feedback effects caused by fluctuations in population size are considered independent of stochastic variation in the environment. We show that an interplay between winter temperature and population density can influence the persistence of a small passerine population under global warming. Although warmer winters favor an increased mean population size, density-dependent feedback can cause the local population to be less buffered against occasional poor environmental conditions (cold winters). This shows that it is essential to go beyond the population size and explore climate effects on the full dynamics to elaborate targeted management actions. PMID:28164157

Microgeographic and temporal genetic variation in populations of the bluetongue virus vector Culicoides variipennis (Diptera: Ceratopogonidae).

PubMed

Tabachnick, W J

1992-05-01

Seven Colorado populations of the bluetongue virus vector Culicoides varipennis (Coquillett) were analyzed for genetic variation at 19-21 isozyme loci. Permanent populations, which overwinter as larvae, showed little temporal genetic change at 19 loci. PGD and MDH showed seasonal changes in gene frequencies, attributable to selection at two permanent populations. Two temporary populations showed low heterozygosity compared with permanent populations. Independent estimates of gene flow, calculated using FST and the private allele method, were Nm* = 2.15 and 6.95, respectively. Colorado C. variipennis permanent populations showed high levels of gene flow which prevented significant genetic differentiation due to genetic drift. Temporary populations showed significant gene frequency differences from nearby permanent populations due to the "founder effect" associated with chance colonization.

Historical overfishing and the recent collapse of coastal ecosystems

USGS Publications Warehouse

Jackson, J.B.C.; Kirby, M.X.; Berger, W.H.; Bjorndal, K.A.; Botsford, L.W.; Bourque, B.J.; Bradbury, R.; Cooke, R.; Erlandson, J.; Estes, J.A.; Hughes, T.P.; Kidwell, S.; Lange, C.B.; Lenihan, H.S.; Pandolfi, J.M.; Peterson, C.H.; Steneck, R.S.; Tegner, M.J.; Warner, R.

2001-01-01

A method for calculating parameters necessary to maintain stable populations is described and the management implications of the method are discussed. This method depends upon knowledge of the population mortality rate schedule, the age at which the species reaches maturity, and recruitment rates or age ratios in the population. Four approaches are presented which yield information about the status of the population: (1) necessary production for a stable population, (2) allowable mortality for a stable population, (3) annual rate of change in population size, and (4) age ratios in the population which yield a stable condition. General formulas for these relationships, and formulas for several special cases, are presented. Tables are also presented showing production required to maintain a stable population with the simpler (more common) mortality and fecundity schedules.

Population control II: The population establishment today.

PubMed

Hartmann, B

1997-01-01

Although population assistance represents a relatively small share of official development assistance, it influences many other aspects of development planning. The organizations that comprise the population establishment have a common purpose--the reduction of population growth in the Third World--but they are not homogeneous and sometimes have conflicting goals and strategies. National governments, multilateral agencies, nongovernmental organizations, foundations, academic centers, and pressure groups all contribute to creating and sustaining what has become a virtual population control industry. Through scholarships, travel grants, awards, and favorable publicity, Third World elites have been encouraged to join the population establishment. The World Bank, the U.S. Agency for International Development, and the U.N. Fund for Population Activities have pursued explicit strategies for pressuring Third World governments to design and implement population policies, most recently in Africa.

Population substructure in Cache County, Utah: the Cache County study

PubMed Central

2014-01-01

Background Population stratification is a key concern for genetic association analyses. In addition, extreme homogeneity of ethnic origins of a population can make it difficult to interpret how genetic associations in that population may translate into other populations. Here we have evaluated the genetic substructure of samples from the Cache County study relative to the HapMap Reference populations and data from the Alzheimer's Disease Neuroimaging Initiative (ADNI). Results Our findings show that the Cache County study is similar in ethnic diversity to the self-reported "Whites" in the ADNI sample and less homogenous than the HapMap CEU population. Conclusions We conclude that the Cache County study is genetically representative of the general European American population in the USA and is an appropriate population for conducting broadly applicable genetic studies. PMID:25078123

Determinants of genetic structure in a nonequilibrium metapopulation of the plant Silene latifolia.

PubMed

Fields, Peter D; Taylor, Douglas R

2014-01-01

Population genetic differentiation will be influenced by the demographic history of populations, opportunities for migration among neighboring demes and founder effects associated with repeated extinction and recolonization. In natural populations, these factors are expected to interact with each other and their magnitudes will vary depending on the spatial distribution and age structure of local demes. Although each of these effects has been individually identified as important in structuring genetic variance, their relative magnitude is seldom estimated in nature. We conducted a population genetic analysis in a metapopulation of the angiosperm, Silene latifolia, from which we had more than 20 years of data on the spatial distribution, demographic history, and extinction and colonization of demes. We used hierarchical Bayesian methods to disentangle which features of the populations contributed to among population variation in allele frequencies, including the magnitude and direction of their effects. We show that population age, long-term size and degree of connectivity all combine to affect the distribution of genetic variance; small, recently-founded, isolated populations contributed most to increase FST in the metapopulation. However, the effects of population size and population age are best understood as being modulated through the effects of connectivity to other extant populations, i.e. FST diminishes as populations age, but at a rate that depends how isolated the population is. These spatial and temporal correlates of population structure give insight into how migration, founder effect and within-deme genetic drift have combined to enhance and restrict genetic divergence in a natural metapopulation.

Different Mutations Endowing Resistance to Acetyl-CoA Carboxylase Inhibitors Results in Changes in Ecological Fitness of Lolium rigidum Populations

PubMed Central

Matzrafi, Maor; Gerson, Ofri; Rubin, Baruch; Peleg, Zvi

2017-01-01

Various mutations altering the herbicide target site (TS), can lead to structural modifications that decrease binding efficiency and results in herbicide resistant weed. In most cases, such a mutation will be associated with ecological fitness penalty under herbicide free environmental conditions. Here we describe the effect of various mutations, endowing resistance to acetyl-CoA carboxylase (ACCase) inhibitors, on the ecological fitness penalty of Lolium rigidum populations. The TS resistant populations, MH (substitution of isoleucine 1781 to leucine) and NO (cysteine 2088 to arginine), were examined and compared to a sensitive population (AL). Grain weight (GW) characterization of individual plants from both MH and NO populations, showed that resistant individuals had significantly lower GW compared with sensitive ones. Under high temperatures, both TS resistant populations exhibited lower germination rate as compared with the sensitive (AL) population. Likewise, early vigor of plants from both TS resistant populations was significantly lower than the one measured in plants of the sensitive population. Under crop-weed intra-species competition, we found an opposite trend in the response of plants from different populations. Relatively to inter-population competition conditions, plants of MH population were less affected and presented higher reproduction abilities compared to plants from both AL and NO populations. On the basis of our results, a non-chemical approach can be taken to favor the sensitive individuals, eventually leading to a decline in resistant individuals in the population. PMID:28690621

Evaluation of Delisting Criteria and Rebuilding Schedules for Snake River Spring/Summer Chinook, Fall Chinook and Sockeye Salmon : Recovery Issues for Threatened and Endangered Snake River Salmon : Technical Report 10 of 11.

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

Cramer, Steven P.; Neeley, Doug

1993-06-01

We develop a framework for distinguishing healthy and threatened populations, and we analyze specific criteria by which these terms can be measured for threatened populations of salmon in the Snake River. We review reports and analyze existing data on listed populations of salmon in the Snake River to establish a framework for two stages of the recovery process: (1) defining de-listing criteria, and (2) estimating the percentage increase in survival that will be necessary for recovery of the population within specified time frames, given the de-listing criteria that must be achieved. We develop and apply a simplified population model tomore » estimate the percentage improvement in survival that will be necessary to achieve different rates of recovery. We considered five main concepts identifying de-listing criteria: (1) minimum population size, (2) rates of population change, (3) number of population subunits, (4) survival rates, and (5) driving variables. In considering minimum population size, we conclude that high variation in survival rates poses a substantially greater probability of causing extinction than does loss of genetic variation. Distinct population subunits exist and affect both the genetic variability of the population and the dynamics of population decline and growth. We distinguish between two types of population subunits, (1) genetic and (2) geographic, and we give examples of their effects on population recovery.« less

Linking vital rates to invasiveness of a perennial herb.

PubMed

Ramula, Satu

2014-04-01

Invaders generally show better individual performance than non-invaders and, therefore, vital rates (survival, growth, fecundity) could potentially be used to predict species invasiveness outside their native range. Comparative studies have usually correlated vital rates with the invasiveness status of species, while few studies have investigated them in relation to population growth rate. Here, I examined the influence of five vital rates (plant establishment, survival, growth, flowering probability, seed production) and their variability (across geographic regions, habitat types, population sizes and population densities) on population growth rate (λ) using data from 37 populations of an invasive, iteroparous herb (Lupinus polyphyllus) in a part of its invaded range in Finland. Variation in vital rates was often related to habitat type and population density. The performance of the populations varied from declining to rapidly increasing independently of habitat type, population size or population density, but differed between regions. The population growth rate increased linearly with plant establishment, and with the survival and growth of vegetative individuals, while the survival of flowering individuals and annual seed production were not related to λ. The vital rates responsible for rapid population growth varied among populations. These findings highlight the importance of both regional and local conditions to plant population dynamics, demonstrating that individual vital rates do not necessarily correlate with λ. Therefore, to understand the role of individual vital rates in a species ability to invade, it is necessary to quantify their effect on population growth rate.

A comparative study of the mobile population in Wuhan and other major cities.

PubMed

Zeng, Y

1997-01-01

This study examined population mobility among residents of 5 cities in China: Wuhan, Beijing, Shanghai, Guangzhou, and Shenzhen. Data were obtained from the 1995 Sample Survey of 1% of Wuhan Population and provincial Statistical Yearbooks. The total mobile population in China has increased from 20-80 million during 1982-95. Shanghai is the largest Chinese city. Beijing has a large proportion of international and internal migrants. Guangzhou is a capital city that was the first to adopt economic reforms. Migration fueled development in Shenzhen. A larger mobile population was related to larger population density. The mobile population was 20% in all cities, 30% of central city population, and 140.5% of the central city of Shenzhen. Beijing and Shanghai had the highest growth rates. Construction accounts for the largest percentage of business-related mobile population in Wuhan, Beijing, and Shanghai. Manufacturing accounts for the largest percentage in Guangzhou and Shenzhen. Most of the mobile population in capital cities such as Wuhan and Guangzhou, originates from within the provinces. The largest percentage of mobile population in Beijing and Shanghai come from adjacent provinces. Guangzhou receives many migrants from adjacent Hong Kong, Macao, and Taiwan. 47.8-78.8% of mobile population were farmers. More migrants are men. Educational levels are low. The mobile population contributes to industry and informational/cultural exchange. The migrants detract from urban areas in population pressure on housing and services, shortages of employment, illegal activities and crime, and unplanned births.

Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae)

USGS Publications Warehouse

Argentina, Jane E.; Angermeier, Paul L.; Hallerman, Eric M.; Welsh, Stuart A.

2018-01-01

Connectivity among stream fish populations allows for exchange of genetic material and helps maintain genetic diversity, adaptive potential and population stability over time. Changes in species demographics and population connectivity have the potential to permanently alter the genetic patterns of stream fish, although these changes through space and time are variable and understudied in small‐bodied freshwater fish.As a spatially widespread, common species of benthic freshwater fish, the variegate darter (Etheostoma variatum) is a model species for documenting how patterns of genetic structure and diversity respond to increasing isolation due to large dams and how scale of study may shape our understanding of these patterns. We sampled variegate darters from 34 sites across their range in the North American Ohio River basin and examined how patterns of genetic structure and diversity within and between populations responded to historical population changes and dams within and between populations.Spatial scale and configuration of genetic structure varied across the eight identified populations, from tributaries within a watershed, to a single watershed, to multiple watersheds that encompass Ohio River mainstem habitats. This multiwatershed pattern of population structuring suggests genetic dispersal across large distances was and may continue to be common, although some populations remain isolated despite no apparent structural dispersal barriers. Populations with low effective population sizes and evidence of past population bottlenecks showed low allelic richness, but diversity patterns were not related to watershed size, a surrogate for habitat availability. Pairwise genetic differentiation (FST) increased with fluvial distance and was related to both historic and contemporary processes. Genetic diversity changes were influenced by underlying population size and stability, and while instream barriers were not strong determinants of genetic structuring or loss of genetic diversity, they reduce population connectivity and may impact long‐term population persistence.The broad spatial scale of this study demonstrated the large spatial extent of some variegate darter populations and indicated that dispersal is more extensive than expected given the movement patterns typically observed for small‐bodied, benthic fish. Dam impacts depended on underlying population size and stability, with larger populations more resilient to genetic drift and allelic richness loss than smaller populations.Other darters that inhabit large river habitats may show similar patterns in landscape‐scale studies, and large river barriers may impact populations of small‐bodied fish more than previously expected. Estimation of dispersal rates and behaviours is critical to conservation of imperilled riverine species such as darters.

Population structure and genetic diversity in natural populations of Theobroma speciosum Willd. Ex Spreng (Malvaceae).

PubMed

Giustina, L D; Luz, L N; Vieira, F S; Rossi, F S; Soares-Lopes, C R A; Pereira, T N S; Rossi, A A B

2014-02-14

The genus Theobroma found in the Amazon region is composed of 22 species, including Theobroma speciosum, better known as cacauí. These species are constantly threatened by forest fragmentation caused by human activities and require conservation strategies and management aimed at preserving them in their natural environments. The main objective of this study was to analyze the population structure and genetic diversity within and between natural populations of T. speciosum by using ISSR molecular markers to understand the population structure of the species. Four natural populations belonging to the Amazon rainforest (BAC, CRO, FLA, and PNA), located in the State of Mato Grosso, were selected. Amplification reactions were performed using 15 ISSR primers. A total of 101 loci were found, of which 54.46% were polymorphic at the species level. The BAC population showed higher genetic diversity (H=0.095 and I=0.144) and higher percentage of polymorphism (28.71%). The populations showed an FST value of 0.604, indicating marked genetic differentiation. The highest genetic variation was found between populations. Gene flow was low between populations, indicating genetic isolation between populations.

The Relation Between Inflation in Type-I and Type-II Error Rate and Population Divergence in Genome-Wide Association Analysis of Multi-Ethnic Populations.

PubMed

Derks, E M; Zwinderman, A H; Gamazon, E R

2017-05-01

Population divergence impacts the degree of population stratification in Genome Wide Association Studies. We aim to: (i) investigate type-I error rate as a function of population divergence (F ST ) in multi-ethnic (admixed) populations; (ii) evaluate the statistical power and effect size estimates; and (iii) investigate the impact of population stratification on the results of gene-based analyses. Quantitative phenotypes were simulated. Type-I error rate was investigated for Single Nucleotide Polymorphisms (SNPs) with varying levels of F ST between the ancestral European and African populations. Type-II error rate was investigated for a SNP characterized by a high value of F ST . In all tests, genomic MDS components were included to correct for population stratification. Type-I and type-II error rate was adequately controlled in a population that included two distinct ethnic populations but not in admixed samples. Statistical power was reduced in the admixed samples. Gene-based tests showed no residual inflation in type-I error rate.

Genetic diversity and variation of Chinese fir from Fujian province and Taiwan, China, based on ISSR markers

PubMed Central

Chen, Yu; Peng, Zhuqing; Wu, Chao; Ma, Zhihui; Ding, Guochang; Cao, Guangqiu; Ruan, Shaoning; Lin, Sizu

2017-01-01

Genetic diversity and variation among 11 populations of Chinese fir from Fujian province and Taiwan were assessed using inter-simple sequence repeat (ISSR) markers to reveal the evolutionary relationship in their distribution range in this report. Analysis of genetic parameters of the different populations showed that populations in Fujian province exhibited a greater level of genetic diversity than did the populations in Taiwan. Compared to Taiwan populations, significant limited gene flow were observed among Fujian populations. An UPGMA cluster analysis showed that the most individuals of Taiwan populations formed a single cluster, whereas 6 discrete clusters were formed by each population from Fujian. All populations were divided into 3 main groups and that all 5 populations from Taiwan were gathered into a subgroup combined with 2 populations, Dehua and Liancheng, formed one of the 3 main groups, which indicated relative stronger relatedness. It is supported by a genetic structure analysis. All those results are suggesting different levels of genetic diversity and variation of Chinese fir between Fujian and Taiwan, and indicating different patterns of evolutionary process and local environmental adaption. PMID:28406956

Genetic diversity and variation of Chinese fir from Fujian province and Taiwan, China, based on ISSR markers.

PubMed

Chen, Yu; Peng, Zhuqing; Wu, Chao; Ma, Zhihui; Ding, Guochang; Cao, Guangqiu; Ruan, Shaoning; Lin, Sizu

2017-01-01

Genetic diversity and variation among 11 populations of Chinese fir from Fujian province and Taiwan were assessed using inter-simple sequence repeat (ISSR) markers to reveal the evolutionary relationship in their distribution range in this report. Analysis of genetic parameters of the different populations showed that populations in Fujian province exhibited a greater level of genetic diversity than did the populations in Taiwan. Compared to Taiwan populations, significant limited gene flow were observed among Fujian populations. An UPGMA cluster analysis showed that the most individuals of Taiwan populations formed a single cluster, whereas 6 discrete clusters were formed by each population from Fujian. All populations were divided into 3 main groups and that all 5 populations from Taiwan were gathered into a subgroup combined with 2 populations, Dehua and Liancheng, formed one of the 3 main groups, which indicated relative stronger relatedness. It is supported by a genetic structure analysis. All those results are suggesting different levels of genetic diversity and variation of Chinese fir between Fujian and Taiwan, and indicating different patterns of evolutionary process and local environmental adaption.

Population and prehistory III: food-dependent demography in variable environments.

PubMed

Lee, Charlotte T; Puleston, Cedric O; Tuljapurkar, Shripad

2009-11-01

The population dynamics of preindustrial societies depend intimately on their surroundings, and food is a primary means through which environment influences population size and individual well-being. Food production requires labor; thus, dependence of survival and fertility on food involves dependence of a population's future on its current state. We use a perturbation approach to analyze the effects of random environmental variation on this nonlinear, age-structured system. We show that in expanding populations, direct environmental effects dominate induced population fluctuations, so environmental variability has little effect on mean hunger levels, although it does decrease population growth. The growth rate determines the time until population is limited by space. This limitation introduces a tradeoff between population density and well-being, so population effects become more important than the direct effects of the environment: environmental fluctuation increases mortality, releasing density dependence and raising average well-being for survivors. We discuss the social implications of these findings for the long-term fate of populations as they transition from expansion into limitation, given that conditions leading to high well-being during growth depress well-being during limitation.

Baluchi and Pakhtun population data of 9 X-chromosomal short tandem repeat loci.

PubMed

Israr, Muhammad; Shahid, Ahmad Ali; Rakha, Allah; Zar, Mian Sahib; Shahzad, Muhammad Saqib; Rahman, Ziaur; Husnain, Tayyab

2016-01-01

Baluchistan is the largest province of Pakistan in terms of area, constituting approximately 44% of the country's total land mass, and the smallest in terms of population, being home to less than 5% of the country's population. Khyber Pakhtunkhwa (KPK) formerly called North-West Frontier Province is located in the north-west of Pakistan having an estimated 13.4% of total population of Pakistan in which Pakhtuns are the major ethnic group. A total of 250 samples from Baluchi population and 250 samples from Pakhtun population were typed for 9 X-chromosomal STR markers: DXS101, DXS6789, DXS7132, DXS7423, DXS7424, DXS8378, GATA31E08, GATA172D05 and HPRTB along with sex typing locus, Amelogenin. A total of 59 alleles were found in Baluchi population while 61 alleles were found in Pakhtun population. This is the first study of the two populations based on these markers and the population data can be used as reference database for Baluchi and Pakhtun populations. Copyright © 2015 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Low migratory connectivity is common in long-distance migrant birds.

PubMed

Finch, Tom; Butler, Simon J; Franco, Aldina M A; Cresswell, Will

2017-05-01

Estimating how much long-distance migrant populations spread out and mix during the non-breeding season (migratory connectivity) is essential for understanding and predicting population dynamics in the face of global change. We quantify variation in population spread and inter-population mixing in long-distance, terrestrial migrant land-bird populations (712 individuals from 98 populations of 45 species, from tagging studies in the Neotropic and Afro-Palearctic flyways). We evaluate the Mantel test as a metric of migratory connectivity, and explore the extent to which variance in population spread can be explained simply by geography. The mean distance between two individuals from the same population during the non-breeding season was 743 km, covering 10-20% of the maximum width of Africa/South America. Individuals from different breeding populations tended to mix during the non-breeding season, although spatial segregation was maintained in species with relatively large non-breeding ranges (and, to a lesser extent, those with low population-level spread). A substantial amount of between-population variation in population spread was predicted simply by geography, with populations using non-breeding zones with limited land availability (e.g. Central America compared to South America) showing lower population spread. The high levels of population spread suggest that deterministic migration tactics are not generally adaptive; this makes sense in the context of the recent evolution of the systems, and the spatial and temporal unpredictability of non-breeding habitat. The conservation implications of generally low connectivity are that the loss (or protection) of any non-breeding site will have a diffuse but widespread effect on many breeding populations. Although low connectivity should engender population resilience to shifts in habitat (e.g. due to climate change), we suggest it may increase susceptibility to habitat loss. We hypothesize that, because a migrant species cannot adapt to both simultaneously, migrants generally may be more susceptible to population declines in the face of concurrent anthropogenic habitat and climate change. © 2017 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

Subgroup analyses of the safety and efficacy of ramucirumab in Japanese and Western patients in RAINBOW: a randomized clinical trial in second-line treatment of gastric cancer.

PubMed

Shitara, Kohei; Muro, Kei; Shimada, Yasuhiro; Hironaka, Shuichi; Sugimoto, Naotoshi; Komatsu, Yoshito; Nishina, Tomohiro; Yamaguchi, Kensei; Segawa, Yoshihiko; Omuro, Yasushi; Tamura, Takao; Doi, Toshihiko; Yukisawa, Seigo; Yasui, Hirofumi; Nagashima, Fumio; Gotoh, Masahiro; Esaki, Taito; Emig, Michael; Chandrawansa, Kumari; Liepa, Astra M; Wilke, Hansjochen; Ichimiya, Yukako; Ohtsu, Atsushi

2016-07-01

We evaluated the safety and efficacy of ramucirumab plus paclitaxel versus placebo plus paclitaxel in patients previously treated for advanced gastric or gastroesophageal junction adenocarcinoma in Japanese and Western subgroups from the RAINBOW trial. Patients received ramucirumab at 8 mg/kg or placebo (days 1 and 15) plus paclitaxel at 80 mg/m(2) (days 1, 8, and 15 of a 28-day cycle). End points were compared between treatment arms within Japanese (N = 140) and Western (N = 398) populations. The incidence of adverse events of grade 3 or higher was higher for ramucirumab plus paclitaxel in both populations (Japanese population, 83.8 % vs 52.1 %; Western population, 79.1 % vs 61.9 %). Neutropenia was the commonest adverse event of grade 3 or higher, with a higher incidence for ramucirumab plus paclitaxel (Japanese population, 66.2 % vs 25.4 %; Western population, 32.1 % vs 14.7 %). The incidence of febrile neutropenia was low and was similar between treatment arms in both populations. The overall survival hazard ratio was 0.88 (95 % confidence interval, 0.60-1.28) in the Japanese population and 0.73 (95 % confidence interval, 0.58-0.91) in the Western population. The progression-free survival hazard ratio was 0.50 (95 % confidence interval, 0.35-0.73) in the Japanese population and 0.63 (95 % confidence interval, 0.51-0.79) in the Western population. The objective response rate was higher for ramucirumab plus paclitaxel in both populations (Japanese population, 41.2 % vs 19.4 %; Western population, 26.8 % vs 13.0 %), as was the 6-month survival rate (Japanese population, 94.1 % vs 71.4 %; Western population, 66.0 % vs 49.0 %). Safety profiles of the ramucirumab plus paclitaxel arm were similar between populations, though there was a higher incidence of neutropenia in Japanese patients. Progression-free survival and objective response rate improvements were observed for ramucirumab plus paclitaxel in both populations. CLINICALTRIALS. NCT01170663.

Tuning stochastic matrix models with hydrologic data to predict the population dynamics of a riverine fish.

PubMed

Sakaris, Peter C; Irwin, Elise R

2010-03-01

We developed stochastic matrix models to evaluate the effects of hydrologic alteration and variable mortality on the population dynamics of a lotic fish in a regulated river system. Models were applied to a representative lotic fish species, the flathead catfish (Pylodictis olivaris), for which two populations were examined: a native population from a regulated reach of the Coosa River (Alabama, USA) and an introduced population from an unregulated section of the Ocmulgee River (Georgia, USA). Size-classified matrix models were constructed for both populations, and residuals from catch-curve regressions were used as indices of year class strength (i.e., recruitment). A multiple regression model indicated that recruitment of flathead catfish in the Coosa River was positively related to the frequency of spring pulses between 283 and 566 m3/s. For the Ocmulgee River population, multiple regression models indicated that year class strength was negatively related to mean March discharge and positively related to June low flow. When the Coosa population was modeled to experience five consecutive years of favorable hydrologic conditions during a 50-year projection period, it exhibited a substantial spike in size and increased at an overall 0.2% annual rate. When modeled to experience five years of unfavorable hydrologic conditions, the Coosa population initially exhibited a decrease in size but later stabilized and increased at a 0.4% annual rate following the decline. When the Ocmulgee River population was modeled to experience five years of favorable conditions, it exhibited a substantial spike in size and increased at an overall 0.4% annual rate. After the Ocmulgee population experienced five years of unfavorable conditions, a sharp decline in population size was predicted. However, the population quickly recovered, with population size increasing at a 0.3% annual rate following the decline. In general, stochastic population growth in the Ocmulgee River was more erratic and variable than population growth in the Coosa River. We encourage ecologists to develop similar models for other lotic species, particularly in regulated river systems. Successful management of fish populations in regulated systems requires that we are able to predict how hydrology affects recruitment and will ultimately influence the population dynamics of fishes.

Population genomics reveals that an anthropophilic population of Aedes aegypti mosquitoes in West Africa recently gave rise to American and Asian populations of this major disease vector.

PubMed

Crawford, Jacob E; Alves, Joel M; Palmer, William J; Day, Jonathan P; Sylla, Massamba; Ramasamy, Ranjan; Surendran, Sinnathamby N; Black, William C; Pain, Arnab; Jiggins, Francis M

2017-02-28

The mosquito Aedes aegypti is the main vector of dengue, Zika, chikungunya and yellow fever viruses. This major disease vector is thought to have arisen when the African subspecies Ae. aegypti formosus evolved from being zoophilic and living in forest habitats into a form that specialises on humans and resides near human population centres. The resulting domestic subspecies, Ae. aegypti aegypti, is found throughout the tropics and largely blood-feeds on humans. To understand this transition, we have sequenced the exomes of mosquitoes collected from five populations from around the world. We found that Ae. aegypti specimens from an urban population in Senegal in West Africa were more closely related to populations in Mexico and Sri Lanka than they were to a nearby forest population. We estimate that the populations in Senegal and Mexico split just a few hundred years ago, and we found no evidence of Ae. aegypti aegypti mosquitoes migrating back to Africa from elsewhere in the tropics. The out-of-Africa migration was accompanied by a dramatic reduction in effective population size, resulting in a loss of genetic diversity and rare genetic variants. We conclude that a domestic population of Ae. aegypti in Senegal and domestic populations on other continents are more closely related to each other than to other African populations. This suggests that an ancestral population of Ae. aegypti evolved to become a human specialist in Africa, giving rise to the subspecies Ae. aegypti aegypti. The descendants of this population are still found in West Africa today, and the rest of the world was colonised when mosquitoes from this population migrated out of Africa. This is the first report of an African population of Ae. aegypti aegypti mosquitoes that is closely related to Asian and American populations. As the two subspecies differ in their ability to vector disease, their existence side by side in West Africa may have important implications for disease transmission.

Estimating Traveler Populations at Airport and Cruise Terminals for Population Distribution and Dynamics

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

Jochem, Warren C; Sims, Kelly M; Bright, Eddie A

In recent years, uses of high-resolution population distribution databases are increasing steadily for environmental, socioeconomic, public health, and disaster-related research and operations. With the development of daytime population distribution, temporal resolution of such databases has been improved. However, the lack of incorporation of transitional population, namely business and leisure travelers, leaves a significant population unaccounted for within the critical infrastructure networks, such as at transportation hubs. This paper presents two general methodologies for estimating passenger populations in airport and cruise port terminals at a high temporal resolution which can be incorporated into existing population distribution models. The methodologies are geographicallymore » scalable and are based on, and demonstrate how, two different transportation hubs with disparate temporal population dynamics can be modeled utilizing publicly available databases including novel data sources of flight activity from the Internet which are updated in near-real time. The airport population estimation model shows great potential for rapid implementation for a large collection of airports on a national scale, and the results suggest reasonable accuracy in the estimated passenger traffic. By incorporating population dynamics at high temporal resolutions into population distribution models, we hope to improve the estimates of populations exposed to or at risk to disasters, thereby improving emergency planning and response, and leading to more informed policy decisions.« less

Patterns of admixture and population structure in native populations of Northwest North America.

PubMed

Verdu, Paul; Pemberton, Trevor J; Laurent, Romain; Kemp, Brian M; Gonzalez-Oliver, Angelica; Gorodezky, Clara; Hughes, Cris E; Shattuck, Milena R; Petzelt, Barbara; Mitchell, Joycelynn; Harry, Harold; William, Theresa; Worl, Rosita; Cybulski, Jerome S; Rosenberg, Noah A; Malhi, Ripan S

2014-08-01

The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas.

Synchrony of Piping Plover breeding populations in the U.S. Northern Great Plains

USGS Publications Warehouse

Roche, Erin A.; Shaffer, Terry L.; Dovichin, Colin M.; Sherfy, Mark H.; Anteau, Michael J.; Wiltermuth, Mark T.

2016-01-01

Local populations that fluctuate synchronously are at a greater risk of extinction than those that do not. The closer the geographic proximity of populations, the more prone they are to synchronizing. Shorebird species select habitat broadly, and many breed across regions with diverse nesting habitat types. Under these conditions, nearby populations may experience conditions sufficiently different to prevent population synchrony, despite dispersal. In the U.S. Northern Great Plains, the Piping Plover (Charadrius melodus), federally listed as Threatened, is a migratory shorebird species that nests on the shorelines of rivers, reservoirs, and alkaline lakes. We assessed the degree to which local plover breeding population abundances were correlated (population synchrony), changed over time (population stability), and were influenced by environmental factors such as available habitat, precipitation, and within-season reservoir level rise. We found that the abundances of breeding populations nesting in riverine and reservoir habitats were the most synchronous, while populations nesting in alkaline lake habitats exhibited the greatest stability. Changes in local breeding population abundances were not explained by a single factor across habitat types. However, the abundances of local populations nesting in alkaline lake and river shoreline habitats were positively correlated with changes in nesting habitat availability. Our results suggest that dispersal among populations nesting in either river or reservoir and alkaline lake shoreline habitat may have an overall stabilizing effect on the persistence of the Great Plains Piping Plover metapopulation.

Parallel tagged next-generation sequencing on pooled samples - a new approach for population genetics in ecology and conservation.

PubMed

Zavodna, Monika; Grueber, Catherine E; Gemmell, Neil J

2013-01-01

Next-generation sequencing (NGS) on pooled samples has already been broadly applied in human medical diagnostics and plant and animal breeding. However, thus far it has been only sparingly employed in ecology and conservation, where it may serve as a useful diagnostic tool for rapid assessment of species genetic diversity and structure at the population level. Here we undertake a comprehensive evaluation of the accuracy, practicality and limitations of parallel tagged amplicon NGS on pooled population samples for estimating species population diversity and structure. We obtained 16S and Cyt b data from 20 populations of Leiopelma hochstetteri, a frog species of conservation concern in New Zealand, using two approaches - parallel tagged NGS on pooled population samples and individual Sanger sequenced samples. Data from each approach were then used to estimate two standard population genetic parameters, nucleotide diversity (π) and population differentiation (FST), that enable population genetic inference in a species conservation context. We found a positive correlation between our two approaches for population genetic estimates, showing that the pooled population NGS approach is a reliable, rapid and appropriate method for population genetic inference in an ecological and conservation context. Our experimental design also allowed us to identify both the strengths and weaknesses of the pooled population NGS approach and outline some guidelines and suggestions that might be considered when planning future projects.

Patterns of Admixture and Population Structure in Native Populations of Northwest North America

PubMed Central

Verdu, Paul; Pemberton, Trevor J.; Laurent, Romain; Kemp, Brian M.; Gonzalez-Oliver, Angelica; Gorodezky, Clara; Hughes, Cris E.; Shattuck, Milena R.; Petzelt, Barbara; Mitchell, Joycelynn; Harry, Harold; William, Theresa; Worl, Rosita; Cybulski, Jerome S.; Rosenberg, Noah A.; Malhi, Ripan S.

2014-01-01

The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas. PMID:25122539

Threshold of long-term survival of a coastal delphinid in anthropogenically degraded environment: Indo-Pacific humpback dolphins in Pearl River Delta.

PubMed

Karczmarski, Leszek; Huang, Shiang-Lin; Chan, Stephen C Y

2017-02-23

Defining demographic and ecological threshold of population persistence can assist in informing conservation management. We undertook such analyses for the Indo-Pacific humpback dolphin (Sousa chinensis) in the Pearl River Delta (PRD) region, southeast China. We use adult survival estimates for assessments of population status and annual rate of change. Our estimates indicate that, given a stationary population structure and minimal risk scenario, ~2000 individuals (minimum viable population in carrying capacity, MVP k ) can maintain the population persistence across 40 generations. However, under the current population trend (~2.5% decline/annum), the population is fast approaching its viability threshold and may soon face effects of demographic stochasticity. The population demographic trajectory and the minimum area of critical habitat (MACH) that could prevent stochastic extinction are both highly sensitive to fluctuations in adult survival. For a hypothetical stationary population, MACH should approximate 3000-km 2 . However, this estimate increases four-fold with a 5% increase of adult mortality and exceeds the size of PRD when calculated for the current population status. On the other hand, cumulatively all current MPAs within PRD fail to secure the minimum habitat requirement to accommodate sufficiently viable population size. Our findings indicate that the PRD population is deemed to become extinct unless effective conservation measures can rapidly reverse the current population trend.

Population size is weakly related to quantitative genetic variation and trait differentiation in a stream fish.

PubMed

Wood, Jacquelyn L A; Tezel, Defne; Joyal, Destin; Fraser, Dylan J

2015-09-01

How population size influences quantitative genetic variation and differentiation among natural, fragmented populations remains unresolved. Small, isolated populations might occupy poor quality habitats and lose genetic variation more rapidly due to genetic drift than large populations. Genetic drift might furthermore overcome selection as population size decreases. Collectively, this might result in directional changes in additive genetic variation (VA ) and trait differentiation (QST ) from small to large population size. Alternatively, small populations might exhibit larger variation in VA and QST if habitat fragmentation increases variability in habitat types. We explored these alternatives by investigating VA and QST using nine fragmented populations of brook trout varying 50-fold in census size N (179-8416) and 10-fold in effective number of breeders, Nb (18-135). Across 15 traits, no evidence was found for consistent differences in VA and QST with population size and almost no evidence for increased variability of VA or QST estimates at small population size. This suggests that (i) small populations of some species may retain adaptive potential according to commonly adopted quantitative genetic measures and (ii) populations of varying sizes experience a variety of environmental conditions in nature, however extremely large studies are likely required before any firm conclusions can be made. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

The Growth of Older Inmate Populations: How Population Aging Explains Rising Age at Admission.

PubMed

Luallen, Jeremy; Cutler, Christopher

2017-09-01

Older inmates are the fastest growing segment of the prison population; however, the reasons for this are not well understood. One explanation is that the general population is aging, driving prison age distributions to change. For this article, we study the role of population aging in prison growth by investigating how the baby boom phenomenon of post-World War II has contributed to the growth of older inmate populations. We identify the impact of population aging using simulation methods that explain prison growth as the combination of criminal justice processes. Overall, we find evidence that population aging has played a significant role in explaining the growth of older inmate populations, in particular among inmates aged between 50 and 64 years, contributing to as much as half of the observed increase in these groups since 2000. This finding stands in contrast to the notion that population aging has little explanatory power in describing the growth of prison populations and implies that older inmate groups are more sensitive to compositional changes in the general population. We argue that prediction-based modeling of prison growth should more seriously consider the impacts and consequences of demographic shifts among older prisoner populations. © The Author 2015. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Classification of stellar populations in globular clusters

NASA Astrophysics Data System (ADS)

Wang, Yue; Zhao, Gang; Li, Hai-Ning

2017-04-01

Possessing multiple stellar populations has been accepted as a common feature of globular clusters (GCs). Different stellar populations manifest themselves with different chemical features, e.g. the well-known O-Na anti-correlation. Generally, the first (primordial) population has O and Na abundances consistent with those of field stars with similar metallicity; while the second (polluted) population is identified by their Na overabundance and O deficiency. The fraction of the populations is an important constraint on the GC formation scenario. Several methods have been proposed for the classification of GC populations. Here we examine a criterion derived based on the distribution of Galactic field stars, which relies on Na abundance as a function of [Fe/H], to distinguish first and second stellar populations in GCs. By comparing the first population fractions of 17 GCs estimated by the field star criterion with those in the literature derived by methods related to individual GCs, we find that the field star criterion tends to overestimate the first population fractions. The population separation methods, which are related to an individual GC sample, are recommended because the diversity of GCs can be taken into consideration. Currently, more caution should be exercised if one wants to regard field stars as a reference for the identification of a GC population. However, further study on the connection between field stars and GCs populations is still needed.

Human Population Problems

ERIC Educational Resources Information Center

Emmel, Thomas C.; Sligh, Michael M.

1970-01-01

Asserts that overpopulation is the most pressing world problem. Topics discussed include population control in primitive societies, population growth and control in modern societies, methods of motivational population control, consequences of no population control, and mass famines during the 1970's in underdeveloped countries. Cities 33…

Combining multiple sources of data to inform conservation of Lesser Prairie-Chicken populations

USGS Publications Warehouse

Ross, Beth; Haukos, David A.; Hagen, Christian A.; Pitman, James

2018-01-01

Conservation of small populations is often based on limited data from spatially and temporally restricted studies, resulting in management actions based on an incomplete assessment of the population drivers. If fluctuations in abundance are related to changes in weather, proper management is especially important, because extreme weather events could disproportionately affect population abundance. Conservation assessments, especially for vulnerable populations, are aided by a knowledge of how extreme events influence population status and trends. Although important for conservation efforts, data may be limited for small or vulnerable populations. Integrated population models maximize information from various sources of data to yield population estimates that fully incorporate uncertainty from multiple data sources while allowing for the explicit incorporation of environmental covariates of interest. Our goal was to assess the relative influence of population drivers for the Lesser Prairie-Chicken (Tympanuchus pallidicinctus) in the core of its range, western and southern Kansas, USA. We used data from roadside lek count surveys, nest monitoring surveys, and survival data from telemetry monitoring combined with climate (Palmer drought severity index) data in an integrated population model. Our results indicate that variability in population growth rate was most influenced by variability in juvenile survival. The Palmer drought severity index had no measurable direct effects on adult survival or mean number of offspring per female; however, there were declines in population growth rate following severe drought. Because declines in population growth rate occurred at a broad spatial scale, declines in response to drought were likely due to decreases in chick and juvenile survival rather than emigration outside of the study area. Overall, our model highlights the importance of accounting for environmental and demographic sources of variability, and provides a thorough method for simultaneously evaluating population demography in response to long-term climate effects.

Region-wide and ecotype-specific differences in demographic histories of threespine stickleback populations, estimated from whole genome sequences.

PubMed

Liu, Shenglin; Hansen, Michael M; Jacobsen, Magnus W

2016-10-01

We analysed 81 whole genome sequences of threespine sticklebacks from Pacific North America, Greenland and Northern Europe, representing 16 populations. Principal component analysis of nuclear SNPs grouped populations according to geographical location, with Pacific populations being more divergent from each other relative to European and Greenlandic populations. Analysis of mitogenome sequences showed Northern European populations to represent a single phylogeographical lineage, whereas Greenlandic and particularly Pacific populations showed admixture between lineages. We estimated demographic history using a genomewide coalescence with recombination approach. The Pacific populations showed gradual population expansion starting >100 Kya, possibly reflecting persistence in cryptic refuges near the present distributional range, although we do not rule out possible influence of ancient admixture. Sharp population declines ca. 14-15 Kya were suggested to reflect founding of freshwater populations by marine ancestors. In Greenland and Northern Europe, demographic expansion started ca. 20-25 Kya coinciding with the end of the Last Glacial Maximum. In both regions, marine and freshwater populations started to show different demographic trajectories ca. 8-9 Kya, suggesting that this was the time of recolonization. In Northern Europe, this estimate was surprisingly late, but found support in subfossil evidence for presence of several freshwater fish species but not sticklebacks 12 Kya. The results demonstrate distinctly different demographic histories across geographical regions with potential consequences for adaptive processes. They also provide empirical support for previous assumptions about freshwater populations being founded independently from large, coherent marine populations, a key element in the Transporter Hypothesis invoked to explain the widespread occurrence of parallel evolution across freshwater stickleback populations. © 2016 John Wiley & Sons Ltd.

Genetic wealth, population health: Major histocompatibility complex variation in captive and wild ring-tailed lemurs (Lemur catta).

PubMed

Grogan, Kathleen E; Sauther, Michelle L; Cuozzo, Frank P; Drea, Christine M

2017-10-01

Across species, diversity at the major histocompatibility complex (MHC) is critical to individual disease resistance and, hence, to population health; however, MHC diversity can be reduced in small, fragmented, or isolated populations. Given the need for comparative studies of functional genetic diversity, we investigated whether MHC diversity differs between populations which are open, that is experiencing gene flow, versus populations which are closed, that is isolated from other populations. Using the endangered ring-tailed lemur ( Lemur catta ) as a model, we compared two populations under long-term study: a relatively "open," wild population ( n  = 180) derived from Bezà Mahafaly Special Reserve, Madagascar (2003-2013) and a "closed," captive population ( n  = 121) derived from the Duke Lemur Center (DLC, 1980-2013) and from the Indianapolis and Cincinnati Zoos (2012). For all animals, we assessed MHC-DRB diversity and, across populations, we compared the number of unique MHC-DRB alleles and their distributions. Wild individuals possessed more MHC-DRB alleles than did captive individuals, and overall, the wild population had more unique MHC-DRB alleles that were more evenly distributed than did the captive population. Despite management efforts to maintain or increase genetic diversity in the DLC population, MHC diversity remained static from 1980 to 2010. Since 2010, however, captive-breeding efforts resulted in the MHC diversity of offspring increasing to a level commensurate with that found in wild individuals. Therefore, loss of genetic diversity in lemurs, owing to small founder populations or reduced gene flow, can be mitigated by managed breeding efforts. Quantifying MHC diversity within individuals and between populations is the necessary first step to identifying potential improvements to captive management and conservation plans.

Uncertainty in Population Estimates for Endangered Animals and Improving the Recovery Process

PubMed Central

Haines, Aaron M.; Zak, Matthew; Hammond, Katie; Scott, J. Michael; Goble, Dale D.; Rachlow, Janet L.

2013-01-01

Simple Summary The objective of our study was to evaluate the mention of uncertainty (i.e., variance) associated with population size estimates within U.S. recovery plans for endangered animals. To do this we reviewed all finalized recovery plans for listed terrestrial vertebrate species. We found that more recent recovery plans reported more estimates of population size and uncertainty. Also, bird and mammal recovery plans reported more estimates of population size and uncertainty. We recommend that updated recovery plans combine uncertainty of population size estimates with a minimum detectable difference to aid in successful recovery. Abstract United States recovery plans contain biological information for a species listed under the Endangered Species Act and specify recovery criteria to provide basis for species recovery. The objective of our study was to evaluate whether recovery plans provide uncertainty (e.g., variance) with estimates of population size. We reviewed all finalized recovery plans for listed terrestrial vertebrate species to record the following data: (1) if a current population size was given, (2) if a measure of uncertainty or variance was associated with current estimates of population size and (3) if population size was stipulated for recovery. We found that 59% of completed recovery plans specified a current population size, 14.5% specified a variance for the current population size estimate and 43% specified population size as a recovery criterion. More recent recovery plans reported more estimates of current population size, uncertainty and population size as a recovery criterion. Also, bird and mammal recovery plans reported more estimates of population size and uncertainty compared to reptiles and amphibians. We suggest the use of calculating minimum detectable differences to improve confidence when delisting endangered animals and we identified incentives for individuals to get involved in recovery planning to improve access to quantitative data. PMID:26479531

Contemporary paternal genetic landscape of Polish and German populations: from early medieval Slavic expansion to post-World War II resettlements.

PubMed

Rębała, Krzysztof; Martínez-Cruz, Begoña; Tönjes, Anke; Kovacs, Peter; Stumvoll, Michael; Lindner, Iris; Büttner, Andreas; Wichmann, H-Erich; Siváková, Daniela; Soták, Miroslav; Quintana-Murci, Lluís; Szczerkowska, Zofia; Comas, David

2013-04-01

Homogeneous Proto-Slavic genetic substrate and/or extensive mixing after World War II were suggested to explain homogeneity of contemporary Polish paternal lineages. Alternatively, Polish local populations might have displayed pre-war genetic heterogeneity owing to genetic drift and/or gene flow with neighbouring populations. Although sharp genetic discontinuity along the political border between Poland and Germany indisputably results from war-mediated resettlements and homogenisation, it remained unknown whether Y-chromosomal diversity in ethnically/linguistically defined populations was clinal or discontinuous before the war. In order to answer these questions and elucidate early Slavic migrations, 1156 individuals from several Slavic and German populations were analysed, including Polish pre-war regional populations and an autochthonous Slavic population from Germany. Y chromosomes were assigned to 39 haplogroups and genotyped for 19 STRs. Genetic distances revealed similar degree of differentiation of Slavic-speaking pre-war populations from German populations irrespective of duration and intensity of contacts with German speakers. Admixture estimates showed minor Slavic paternal ancestry (~20%) in modern eastern Germans and hardly detectable German paternal ancestry in Slavs neighbouring German populations for centuries. BATWING analysis of isolated Slavic populations revealed that their divergence was preceded by rapid demographic growth, undermining theory that Slavic expansion was primarily linguistic rather than population spread. Polish pre-war regional populations showed within-group heterogeneity and lower STR variation within R-M17 subclades compared with modern populations, which might have been homogenised by war resettlements. Our results suggest that genetic studies on early human history in the Vistula and Oder basins should rely on reconstructed pre-war rather than modern populations.

[Population viability of Alouatta palliata (Primates: Atelidae) and Cebus capucinus (Primates: Cebidae) at Refugio de Vida Silvestre Privado Nogal, Sarapiquí, Heredia, Costa Rica].

PubMed

Rodríguez-Matamoros, Jorge; Villalobos-Brenes, Federico; Gutiérrez-Espeleta, Gustavo A

2012-06-01

Habitat destruction may cause wildlife population fragmentation and is considered an important factor in small population species extinction. As wildlife populations become smaller, threats to their stability and persistence arise as a result of demographic, environmental and genetic stochastic factors. The aim of this work was to study the effects of population fragmentation on the long term viability of Alouatta palliata and Cebus capucinus populations, at Refugio de Vida Silvestre Privado Nogal, Sarapiquí (RVSPN), Heredia. For this we used the computer software VORTEX to run a population viability analysis (PVA) for both species. The input data of the PVA were taken from the demography structure of the RVSPN, literature sources from the species and from PVA related papers. We evaluated two sets of scenarios: small fragmented populations to reflect the population current state, and one larger and continuous population, to reflect the effect of reforestation actions followed by RVSPN to connect forest fragments. Results suggest that both A. palliata and C. capucinus can survive in isolated forest fragments. However, if different factors as inbreeding depression, catastrophes or habitat loss were incorporated to the scenarios, the small fragmented populations become unstable and the risk of extinction increased for both species. Continuous and larger populations were more robust against the threats incorporated in the scenarios when compared to the current situation of smaller and fragmented populations. The best management option for both species would be to continue reforestation efforts in the area to connect forest fragments, with the result of larger and continuous populations of both species. It is important to continue the observation of both species populations, and to promote a habitat management to reduce the negative effects of stochastic environmental events.

New summer areas and mixing of two greater sandhill crane populations in the Intermountain West

USGS Publications Warehouse

Collins, Daniel P.; Grisham, Blake A.; Conring, Courtenay M.; Knetter, Jeffrey M.; Conway, Warren C.; Carleton, Scott A.; Boggie, Matthew A.

2016-01-01

Population delineation throughout the annual life cycle for migratory birds is needed to formulate regional and national management and conservation strategies. Despite being well studied continentally, connectivity of sandhill crane Grus canadensis populations throughout the western portion of their North American range remains poorly described. Our objectives were to 1) use global positioning system satellite transmitter terminals to identify summer distributions for the Lower Colorado River Valley Population of greater sandhill cranes Grus canadensis tabida and 2) determine whether intermingling occurs among any of the western greater sandhill crane populations: Rocky Mountain Population, Lower Colorado River Valley Population, and Central Valley Population. Capture and marking occurred during winter and summer on private lands in California and Idaho as well as on two National Wildlife Refuges: Cibola and Sonny Bono Salton Sea National Wildlife Refuges. A majority of marked greater sandhill cranes summered in what is established Lower Colorado River Valley Population breeding areas in northeastern Nevada and southwestern Idaho. A handful of greater sandhill cranes summered outside of traditional breeding areas in west-central Idaho around Cascade Reservoir near Donnelly and Cascade, Idaho. For example, a greater sandhill crane colt captured near Donnelly in July 2014 survived to winter migration and moved south to areas associated with the Rocky Mountain Population. The integration of the greater sandhill crane colt captured near Donnelly provides the first evidence of potential intermingling between the Lower Colorado River Population and Rocky Mountain Population. We suggest continued marking and banding efforts of all three western populations of greater sandhill cranes will accurately delineate population boundaries and connectivity and inform management decisions for the three populations.

Stock enhancement or sea ranching? Insights from monitoring the genetic diversity, relatedness and effective population size in a seeded great scallop population (Pecten maximus).

PubMed

Morvezen, R; Boudry, P; Laroche, J; Charrier, G

2016-09-01

The mass release of hatchery-propagated stocks raises numerous questions concerning its efficiency in terms of local recruitment and effect on the genetic diversity of wild populations. A seeding program, consisting of mass release of hatchery-produced juveniles in the local naturally occurring population of great scallops (Pecten maximus L.), was initiated in the early 1980s in the Bay of Brest (France). The present study aims at evaluating whether this seeding program leads to actual population enhancement, with detectable effects on genetic diversity and effective population size, or consists of sea ranching with limited genetic consequences on the wild stock. To address this question, microsatellite-based genetic monitoring of three hatchery-born and naturally recruited populations was conducted over a 5-year period. Results showed a limited reduction in allelic richness but a strong alteration of allelic frequencies in hatchery populations, while genetic diversity appeared very stable over time in the wild populations. A temporal increase in relatedness was observed in both cultured stock and wild populations. Effective population size (Ne) estimates were low and variable in the wild population. Moreover, the application of the Ryman-Laikre model suggested a high contribution of hatchery-born scallops to the reproductive output of the wild population. Overall, the data suggest that the main objective of the seeding program, which is stock enhancement, is fulfilled. Moreover, gene flow from surrounding populations and/or the reproductive input of undetected sub-populations within the bay may buffer the Ryman-Laikre effect and ensure the retention of the local genetic variability.

Marshes as “Mountain Tops”: Genetic Analyses of the Critically Endangered São Paulo Marsh Antwren (Aves: Thamnophilidae)

PubMed Central

de Camargo, Crisley; Gibbs, H. Lisle; Costa, Mariellen C.; Del-Rio, Glaucia; Silveira, Luís F.

2015-01-01

Small populations of endangered species can be impacted by genetic processes such as drift and inbreeding that reduce population viability. As such, conservation genetic analyses that assess population levels of genetic variation and levels of gene flow can provide important information for managing threatened species. The São Paulo Marsh Antwren (Formicivora paludicola) is a recently-described and critically endangered bird from São Paulo State (Brazil) whose total estimated population is around 250–300 individuals, distributed in only 15 isolated marshes around São Paulo metropolitan region. We used microsatellite DNA markers to estimate the population genetic characteristics of the three largest remaining populations of this species all within 60 km of each other. We detected a high and significant genetic structure between all populations (overall F ST = 0.103) which is comparable to the highest levels of differentiation ever documented for birds, (e.g., endangered birds found in isolated populations on the tops of African mountains), but also evidence for first-generation immigrants, likely from small local unsampled populations. Effective population sizes were small (between 28.8–99.9 individuals) yet there are high levels of genetic variability within populations and no evidence for inbreeding. Conservation implications of this work are that the high levels of genetic structure suggests that translocations between populations need to be carefully considered in light of possible local adaptation and that remaining populations of these birds should be managed as conservation units that contain both main populations studied here but also small outlying populations which may be a source of immigrants. PMID:26447791

Effective Population Size, Genetic Variation, and Their Relevance for Conservation: The Bighorn Sheep in Tiburon Island and Comparisons with Managed Artiodactyls

PubMed Central

Gasca-Pineda, Jaime; Cassaigne, Ivonne; Alonso, Rogelio A.; Eguiarte, Luis E.

2013-01-01

The amount of genetic diversity in a finite biological population mostly depends on the interactions among evolutionary forces and the effective population size (N e) as well as the time since population establishment. Because the N e estimation helps to explore population demographic history, and allows one to predict the behavior of genetic diversity through time, N e is a key parameter for the genetic management of small and isolated populations. Here, we explored an N e-based approach using a bighorn sheep population on Tiburon Island, Mexico (TI) as a model. We estimated the current (N crnt) and ancestral stable (N stbl) inbreeding effective population sizes as well as summary statistics to assess genetic diversity and the demographic scenarios that could explain such diversity. Then, we evaluated the feasibility of using TI as a source population for reintroduction programs. We also included data from other bighorn sheep and artiodactyl populations in the analysis to compare their inbreeding effective size estimates. The TI population showed high levels of genetic diversity with respect to other managed populations. However, our analysis suggested that TI has been under a genetic bottleneck, indicating that using individuals from this population as the only source for reintroduction could lead to a severe genetic diversity reduction. Analyses of the published data did not show a strict correlation between H E and N crnt estimates. Moreover, we detected that ancient anthropogenic and climatic pressures affected all studied populations. We conclude that the estimation of N crnt and N stbl are informative genetic diversity estimators and should be used in addition to summary statistics for conservation and population management planning. PMID:24147115

Contemporary paternal genetic landscape of Polish and German populations: from early medieval Slavic expansion to post-World War II resettlements

PubMed Central

Rębała, Krzysztof; Martínez-Cruz, Begoña; Tönjes, Anke; Kovacs, Peter; Stumvoll, Michael; Lindner, Iris; Büttner, Andreas; Wichmann, H-Erich; Siváková, Daniela; Soták, Miroslav; Quintana-Murci, Lluís; Szczerkowska, Zofia; Comas, David

2013-01-01

Homogeneous Proto-Slavic genetic substrate and/or extensive mixing after World War II were suggested to explain homogeneity of contemporary Polish paternal lineages. Alternatively, Polish local populations might have displayed pre-war genetic heterogeneity owing to genetic drift and/or gene flow with neighbouring populations. Although sharp genetic discontinuity along the political border between Poland and Germany indisputably results from war-mediated resettlements and homogenisation, it remained unknown whether Y-chromosomal diversity in ethnically/linguistically defined populations was clinal or discontinuous before the war. In order to answer these questions and elucidate early Slavic migrations, 1156 individuals from several Slavic and German populations were analysed, including Polish pre-war regional populations and an autochthonous Slavic population from Germany. Y chromosomes were assigned to 39 haplogroups and genotyped for 19 STRs. Genetic distances revealed similar degree of differentiation of Slavic-speaking pre-war populations from German populations irrespective of duration and intensity of contacts with German speakers. Admixture estimates showed minor Slavic paternal ancestry (∼20%) in modern eastern Germans and hardly detectable German paternal ancestry in Slavs neighbouring German populations for centuries. BATWING analysis of isolated Slavic populations revealed that their divergence was preceded by rapid demographic growth, undermining theory that Slavic expansion was primarily linguistic rather than population spread. Polish pre-war regional populations showed within-group heterogeneity and lower STR variation within R-M17 subclades compared with modern populations, which might have been homogenised by war resettlements. Our results suggest that genetic studies on early human history in the Vistula and Oder basins should rely on reconstructed pre-war rather than modern populations. PMID:22968131

Population-focused nursing: advocacy for vulnerable populations in an RN-BSN program.

PubMed

Jones, Melissa; Smith, Paul

2014-01-01

The purpose of this article is to describe an innovative learning activity for online RN-BSN students designed to foster advocacy for vulnerable populations. The Vulnerable Population Advocacy Assignment, included as a component of the online Population-Focused Nursing class, provides students with the opportunity to identify and develop an awareness of issues impacting vulnerable populations and to advocate for policy changes that will influence the health of individuals, families, and populations. RN-BSN students build on previous knowledge and skills in professional communication and advocacy as they develop a policy statement designed to address health disparities impacting local, national, and global populations. © 2014 Wiley Periodicals, Inc.

Making It Count: Improving Estimates of the Size of Transgender and Gender Nonconforming Populations.

PubMed

Deutsch, Madeline B

2016-06-01

An accurate estimate of the number of transgender and gender nonconforming people is essential to inform policy and funding priorities and decisions. Historical reports of population sizes of 1 in 4000 to 1 in 50,000 have been based on clinical populations and likely underestimate the size of the transgender population. More recent population-based studies have found a 10- to 100-fold increase in population size. Studies that estimate population size should be population based, employ the two-step method to allow for collection of both gender identity and sex assigned at birth, and include measures to capture the range of transgender people with nonbinary gender identities.

Behavioral consequences of disasters: a five-stage model of population behavior.

PubMed

Rudenstine, Sasha; Galea, Sandro

2014-12-01

We propose a model of population behavior in the aftermath of disasters. We conducted a qualitative analysis of an empirical dataset of 339 disasters throughout the world spanning from 1950 to 2005. We developed a model of population behavior that is based on 2 fundamental assumptions: (i) behavior is predictable and (ii) population behavior will progress sequentially through 5 stages from the moment the hazard begins until is complete. Understanding the progression of population behavior during a disaster can improve the efficiency and appropriateness of institutional efforts aimed at population preservation after large-scale traumatic events. Additionally, the opportunity for population-level intervention in the aftermath of such events will improve population health.

Population momentum across vertebrate life histories

USGS Publications Warehouse

Koons, D.N.; Grand, J.B.; Arnold, J.M.

2006-01-01

Population abundance is critically important in conservation, management, and demographic theory. Thus, to better understand how perturbations to the life history affect long-term population size, we examined population momentum for four vertebrate classes with different life history strategies. In a series of demographic experiments we show that population momentum generally has a larger effect on long-term population size for organisms with long generation times than for organisms with short generation times. However, patterns between population momentum and generation time varied across taxonomic groups and according to the life history parameter that was changed. Our findings indicate that momentum may be an especially important aspect of population dynamics for long-lived vertebrates, and deserves greater attention in life history studies. Further, we discuss the importance of population momentum in natural resource management, pest control, and conservation arenas. ?? 2006 Elsevier B.V. All rights reserved.

NASA Orbital Debris Baseline Populations

NASA Technical Reports Server (NTRS)

Krisko, Paula H.; Vavrin, A. B.

2013-01-01

The NASA Orbital Debris Program Office has created high fidelity populations of the debris environment. The populations include objects of 1 cm and larger in Low Earth Orbit through Geosynchronous Transfer Orbit. They were designed for the purpose of assisting debris researchers and sensor developers in planning and testing. This environment is derived directly from the newest ORDEM model populations which include a background derived from LEGEND, as well as specific events such as the Chinese ASAT test, the Iridium 33/Cosmos 2251 accidental collision, the RORSAT sodium-potassium droplet releases, and other miscellaneous events. It is the most realistic ODPO debris population to date. In this paper we present the populations in chart form. We describe derivations of the background population and the specific populations added on. We validate our 1 cm and larger Low Earth Orbit population against SSN, Haystack, and HAX radar measurements.

Gene flow and genetic structure in the Galician population (NW Spain) according to Alu insertions

PubMed Central

Varela, Tito A; Fariña, José; Diéguez, Lois Pérez; Lodeiro, Rosa

2008-01-01

Background The most recent Alu insertions reveal different degrees of polymorphism in human populations, and a series of characteristics that make them particularly suitable genetic markers for Human Biology studies. This has led these polymorphisms to be used to analyse the origin and phylogenetic relationships between contemporary human groups. This study analyses twelve Alu sequences in a sample of 216 individuals from the autochthonous population of Galicia (NW Spain), with the aim of studying their genetic structure and phylogenetic position with respect to the populations of Western and Central Europe and North Africa, research that is of special interest in revealing European population dynamics, given the peculiarities of the Galician population due to its geographical situation in western Europe, and its historical vicissitudes. Results The insertion frequencies of eleven of the Alu elements analysed were within the variability range of European populations, while Yb8NBC125 proved to be the lowest so far recorded to date in Europe. Taking the twelve polymorphisms into account, the GD value for the Galician population was 0.268. The comparative analyses carried out using the MDS, NJ and AMOVA methods reveal the existence of spatial heterogeneity, and identify three population groups that correspond to the geographic areas of Western-Central Europe, Eastern Mediterranean Europe and North Africa. Galicia is shown to be included in the Western-Central European cluster, together with other Spanish populations. When only considering populations from Mediterranean Europe, the Galician population revealed a degree of genetic flow similar to that of the majority of the populations from this geographic area. Conclusion The results of this study reveal that the Galician population, despite its geographic situation in the western edge of the European continent, occupies an intermediate position in relation to other European populations in general, and Iberian populations in particular. This confirms the important role that migratory movements have had in the European gene pool, at least since Neolithic times. In turn, the MDS and NJ analyses place Galicia within the group comprised of Western-Central European populations, which is justified by the influence of Germanic peoples on the Galician population during the Middle Ages. However, it should also be noted that some of the markers analysed have a certain degree of differentiation, possibly due to the region's position as a 'cul-de-sac' in terms of Iberian population dynamics. PMID:19055739

Community characteristics that attract physicians in Japan: a cross-sectional analysis of community demographic and economic factors.

PubMed

Matsumoto, Masatoshi; Inoue, Kazuo; Noguchi, Satomi; Toyokawa, Satoshi; Kajii, Eiji

2009-02-18

In many countries, there is a surplus of physicians in some communities and a shortage in others. Population size is known to be correlated with the number of physicians in a community, and is conventionally considered to represent the power of communities to attract physicians. However, associations between other demographic/economic variables and the number of physicians in a community have not been fully evaluated. This study seeks other parameters that correlate with the physician population and show which characteristics of a community determine its "attractiveness" to physicians. Associations between the number of physicians and selected demographic/economic/life-related variables of all of Japan's 3132 municipalities were examined. In order to exclude the confounding effect of community size, correlations between the physician-to-population ratio and other variable-to-population ratios or variable-to-area ratios were evaluated with simple correlation and multiple regression analyses. The equity of physician distribution against each variable was evaluated by the orenz curve and Gini index. Among the 21 variables selected, the service industry workers-to-population ratio (0.543), commercial land price (0.527), sales of goods per person (0.472), and daytime population density (0.451) were better correlated with the physician-to-population ratio than was population density (0.409). Multiple regression analysis showed that the service industry worker-to-population ratio, the daytime population density, and the elderly rate were each independently correlated with the physician-to-population ratio (standardized regression coefficient 0.393, 0.355, 0.089 respectively; each p<0.001). Equity of physician distribution was higher against service industry population (Gini index=0.26) and daytime population (0.28) than against population (0.33). Daytime population and service industry population in a municipality are better parameters of community attractiveness to physicians than population. Because attractiveness is supposed to consist of medical demand and the amenities of urban life, the two parameters may represent the amount of medical demand and/or the extent of urban amenities of the community more precisely than population does. The conventional demand-supply analysis based solely on population as the demand parameter may overestimate the inequity of the physician distribution among communities.

Gene flow and genetic structure in the Galician population (NW Spain) according to Alu insertions.

PubMed

Varela, Tito A; Fariña, José; Diéguez, Lois Pérez; Lodeiro, Rosa

2008-12-02

The most recent Alu insertions reveal different degrees of polymorphism in human populations, and a series of characteristics that make them particularly suitable genetic markers for Human Biology studies. This has led these polymorphisms to be used to analyse the origin and phylogenetic relationships between contemporary human groups. This study analyses twelve Alu sequences in a sample of 216 individuals from the autochthonous population of Galicia (NW Spain), with the aim of studying their genetic structure and phylogenetic position with respect to the populations of Western and Central Europe and North Africa, research that is of special interest in revealing European population dynamics, given the peculiarities of the Galician population due to its geographical situation in western Europe, and its historical vicissitudes. The insertion frequencies of eleven of the Alu elements analysed were within the variability range of European populations, while Yb8NBC125 proved to be the lowest so far recorded to date in Europe. Taking the twelve polymorphisms into account, the GD value for the Galician population was 0.268. The comparative analyses carried out using the MDS, NJ and AMOVA methods reveal the existence of spatial heterogeneity, and identify three population groups that correspond to the geographic areas of Western-Central Europe, Eastern Mediterranean Europe and North Africa. Galicia is shown to be included in the Western-Central European cluster, together with other Spanish populations. When only considering populations from Mediterranean Europe, the Galician population revealed a degree of genetic flow similar to that of the majority of the populations from this geographic area. The results of this study reveal that the Galician population, despite its geographic situation in the western edge of the European continent, occupies an intermediate position in relation to other European populations in general, and Iberian populations in particular. This confirms the important role that migratory movements have had in the European gene pool, at least since Neolithic times. In turn, the MDS and NJ analyses place Galicia within the group comprised of Western-Central European populations, which is justified by the influence of Germanic peoples on the Galician population during the Middle Ages. However, it should also be noted that some of the markers analysed have a certain degree of differentiation, possibly due to the region's position as a 'cul-de-sac' in terms of Iberian population dynamics.

Nepal [Population education in countries of the region].

PubMed

Rongong, R K

1982-06-01

In 1979 the Ministry of Education and Culture in Nepal, in collaboration with Unesco and the UN Fund for Population Activities (UNFPA), organized a National Planning and Development Meeting in Population Education. The objectives were to understand the concept and nature of population education and population education programs in Asia, to review the existing programs of population education initiated by various agencies in Nepal, and to develop guidelines for the formulation of a national population education program, both in school and out of school. All of these objectives were realized. Subsequently, a population education project was formulated for UNFPA funding, with the help of the Unesco Regional Team on Population Education. The primary goal of the project is to gear the entire system--formal and nonformal--to the realization of the potential role of education in the development efforts of the country and the interrelationships between the population situation and different aspects of quality of life at the micro and macro levels. The long range objectives of the program are as follows: develop in the target audience an insight into the interrelationships between population growth and the process of social and economic development at the individual, family, society, national, and international levels; develop desirable attitudes and behavior in the teachers, students, and the community at large towards population issues so that they may make rational decisions about their family size and the quality of life that they would like to have; and institutionalize population education in the formal education system, including university, and the nonformal education program of the Ministry of Education. In a 1981 population education curriculum development workshop, 2 further objectives were added: develop in learners a knowledge and understanding of basic concepts, processes, and measures; and develop among learners an awareness of the attitudes, beliefs, and values affecting decision making on population issues and problems. The key personnel identified to staff the different units implementing population education had no prior training and experience in population education. 3 modalities of training were deemed necessary: an intensive training program for the project staff; orientation for key administrators; and an intercountry study visit. Population education is beginning to take root in the formal and nonformal education system and is regarded as a crucial complementary program to family planning and other population programs in Nepal.

EFFECTS OF CHRONIC STRESS ON WILDLIFE POPULATIONS: A POPULATION MODELING APPROACH AND CASE STUDY

EPA Science Inventory

This chapter describes a matrix modeling approach to characterize and project risks to wildlife populations subject to chronic stress. Population matrix modeling was used to estimate effects of one class of environmental contaminants, dioxin-like compounds (DLCs), to populations ...

Why Population in 1974?

ERIC Educational Resources Information Center

O'Connor, Marion

1974-01-01

Discusses the impact of world population growth leading to the establishment of the United Nations Fund for Population Activities and to the declaration of 1974 as World Population Year. Previews some of the parameters and interconnecting interests to be considered during this year of intensive population study. (JR)

Detecting directional selection in the presence of recent admixture in African-Americans.

PubMed

Lohmueller, Kirk E; Bustamante, Carlos D; Clark, Andrew G

2011-03-01

We investigate the performance of tests of neutrality in admixed populations using plausible demographic models for African-American history as well as resequencing data from African and African-American populations. The analysis of both simulated and human resequencing data suggests that recent admixture does not result in an excess of false-positive results for neutrality tests based on the frequency spectrum after accounting for the population growth in the parental African population. Furthermore, when simulating positive selection, Tajima's D, Fu and Li's D, and haplotype homozygosity have lower power to detect population-specific selection using individuals sampled from the admixed population than from the nonadmixed population. Fay and Wu's H test, however, has more power to detect selection using individuals from the admixed population than from the nonadmixed population, especially when the selective sweep ended long ago. Our results have implications for interpreting recent genome-wide scans for positive selection in human populations. © 2011 by the Genetics Society of America

Towards population-level conservation in the critically endangered Antarctic blue whale: the number and distribution of their populations

PubMed Central

Attard, Catherine R. M.; Beheregaray, Luciano B.; Möller, Luciana M.

2016-01-01

Population-level conservation is required to prevent biodiversity loss within a species, but it first necessitates determining the number and distribution of populations. Many whale populations are still depleted due to 20th century whaling. Whales are one of the most logistically difficult and expensive animals to study because of their mobility, pelagic lifestyle and often remote habitat. We tackle the question of population structure in the Antarctic blue whale (Balaenoptera musculus intermedia) – a critically endangered subspecies and the largest extant animal – by capitalizing on the largest genetic dataset to date for Antarctic blue whales. We found evidence of three populations that are sympatric in the Antarctic feeding grounds and likely occupy separate breeding grounds. Our study adds to knowledge of population structure in the Antarctic blue whale. Future research should invest in locating the breeding grounds and migratory routes of Antarctic blue whales through satellite telemetry to confirm their population structure and allow population-level conservation. PMID:26951747

Genetic analysis of eight population groups living in Taiwan using a 13 X-chromosomal STR loci multiplex system.

PubMed

Hwa, Hsiao-Lin; Lee, James Chun-I; Chang, Yih-Yuan; Yin, Hsiang-Yi; Chen, Ya-Hui; Tseng, Li-Hui; Su, Yi-Ning; Ko, Tsang-Ming

2011-01-01

A 13 X-chromosomal short tandem repeat (STR) multiplex system (DXS6807, DXS8378, DSX9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7424, DXS101, GATA172D05, HPRTB, DXS8377, and DXS7423) was tested on 1,037 DNA samples from eight population groups currently living in Taiwan. Different distributions of the allelic frequencies in different populations were presented. DXS8377 and DXS101 were the two most polymorphic loci in these eight populations, whereas DXS7423 was the least informative marker in most of the populations studied. The genetic distances between the populations and the constructed phylogenetic tree revealed a long genetic distance between Asian and Caucasian populations as well as isolation of the Tao population. The phylogenetic tree grouped populations into clusters compatible with their ethnogeographic relationships. This 13 X-chromosomal short tandem repeat multiplex system offers a considerable number of polymorphic patterns in different populations. This system can be useful in forensic identification casework and ethnogeographic research.

Towards population-level conservation in the critically endangered Antarctic blue whale: the number and distribution of their populations

NASA Astrophysics Data System (ADS)

Attard, Catherine R. M.; Beheregaray, Luciano B.; Möller, Luciana M.

2016-03-01

Population-level conservation is required to prevent biodiversity loss within a species, but it first necessitates determining the number and distribution of populations. Many whale populations are still depleted due to 20th century whaling. Whales are one of the most logistically difficult and expensive animals to study because of their mobility, pelagic lifestyle and often remote habitat. We tackle the question of population structure in the Antarctic blue whale (Balaenoptera musculus intermedia) - a critically endangered subspecies and the largest extant animal - by capitalizing on the largest genetic dataset to date for Antarctic blue whales. We found evidence of three populations that are sympatric in the Antarctic feeding grounds and likely occupy separate breeding grounds. Our study adds to knowledge of population structure in the Antarctic blue whale. Future research should invest in locating the breeding grounds and migratory routes of Antarctic blue whales through satellite telemetry to confirm their population structure and allow population-level conservation.

Population limitation in a non-cyclic arctic fox population in a changing climate.

PubMed

Pálsson, Snæbjörn; Hersteinsson, Páll; Unnsteinsdóttir, Ester R; Nielsen, Ólafur K

2016-04-01

Arctic foxes Vulpes lagopus (L.) display a sharp 3- to 5-year fluctuation in population size where lemmings are their main prey. In areas devoid of lemmings, such as Iceland, they do not experience short-term fluctuations. This study focusses on the population dynamics of the arctic fox in Iceland and how it is shaped by its main prey populations. Hunting statistics from 1958-2003 show that the population size of the arctic fox was at a maximum in the 1950s, declined to a minimum in the 1970s, and increased steadily until 2003. Analysis of the arctic fox population size and their prey populations suggests that fox numbers were limited by rock ptarmigan numbers during the decline period. The recovery of the arctic fox population was traced mostly to an increase in goose populations, and favourable climatic conditions as reflected by the Subpolar Gyre. These results underscore the flexibility of a generalist predator and its responses to shifting food resources and climate changes.

WKB theory of large deviations in stochastic populations

NASA Astrophysics Data System (ADS)

Assaf, Michael; Meerson, Baruch

2017-06-01

Stochasticity can play an important role in the dynamics of biologically relevant populations. These span a broad range of scales: from intra-cellular populations of molecules to population of cells and then to groups of plants, animals and people. Large deviations in stochastic population dynamics—such as those determining population extinction, fixation or switching between different states—are presently in a focus of attention of statistical physicists. We review recent progress in applying different variants of dissipative WKB approximation (after Wentzel, Kramers and Brillouin) to this class of problems. The WKB approximation allows one to evaluate the mean time and/or probability of population extinction, fixation and switches resulting from either intrinsic (demographic) noise, or a combination of the demographic noise and environmental variations, deterministic or random. We mostly cover well-mixed populations, single and multiple, but also briefly consider populations on heterogeneous networks and spatial populations. The spatial setting also allows one to study large fluctuations of the speed of biological invasions. Finally, we briefly discuss possible directions of future work.

Genetic portrait of Jewish populations based on three sets of X-chromosome markers: Indels, Alu insertions and STRs.

PubMed

Ferragut, J F; Bentayebi, K; Pereira, R; Castro, J A; Amorim, A; Ramon, C; Picornell, A

2017-11-01

Population genetic data for 53 X-chromosome markers (32 X-indels, 9 X-Alu insertions and 12 X-STRs) are reported for five populations with Jewish ancestry (Sephardim, North African Jews, Middle Eastern Jews, Ashkenazim, and Chuetas) and Majorca, as the host population of Chuetas. Genetic distances between these populations demonstrated significant differences, except between Sephardic and North African Jews, with the Chuetas as the most differentiated group, in accordance with the particular demographic history of this population. X-chromosome analysis and a comparison with autosomal data suggest a generally sex-biased demographic history in Jewish populations. Asymmetry was found between female and male effective population sizes both in the admixture processes between Jewish communities, and between them and their respective non-Jewish host populations. Results further show that these X-linked markers are highly informative for forensic purposes, and highlight the need for specific databases for differentiated Jewish populations. Copyright © 2017 Elsevier B.V. All rights reserved.

Farm Population of the United States: 1977. Current Population Reports: Farm Population.

ERIC Educational Resources Information Center

Banks, Vera J.; DeAre, Diana

The farm population has declined fairly steadily for more than half a century. By 1970 the proportion of the U.S. population residing on farms had fallen to about 5 per cent, and by 1977 had dropped to 3.6 per cent. About 1.4 per cent of the farm population was of Spanish origin (represented for the first time in this year's report), as compared…

Population remains top priority for China.

PubMed

Li, H

1998-04-01

China, whose population was 430 million in 1840, is facing a population total of 1.3 billion in 2000. Population increased rapidly in the country during the 1950s, but early efforts at population control were abandoned from the start of the Cultural Revolution in 1966 until the 1970s. Today, the importance of family planning (FP) is recognized throughout Chinese society. With 20 million newborns adding 13 million people to the population each year, controlling the population increase will remain a top priority of China's population policy. Other priorities include 1) increasing the quality of life of the population by improving health, promoting literacy, and developing human resources; 2) facing the impact of population aging; 3) struggling to overcome the poverty experienced by 50 million people; and 4) dealing with the imbalanced sex ratio of newborns. China has been attempting to institute strategies to implement the Program of Action adopted by the 1994 International Conference on Population and Development and is attempting to adopt an integrated approach to population programs that combines FP with development measures and the delivery of multiple services to enhance reproductive health. Since 1984, China has worked with Japan's JOICFP on an Integrated Project that offers FP, maternal and child health services, and parasite control.

Genomic copy number variations in three Southeast Asian populations.

PubMed

Ku, Chee-Seng; Pawitan, Yudi; Sim, Xueling; Ong, Rick T H; Seielstad, Mark; Lee, Edmund J D; Teo, Yik-Ying; Chia, Kee-Seng; Salim, Agus

2010-07-01

Research on the role of copy number variations (CNVs) in the genetic risk of diseases in Asian populations has been hampered by a relative lack of reference CNV maps for Asian populations outside the East Asians. In this article, we report the population characteristics of CNVs in Chinese, Malay, and Asian Indian populations in Singapore. Using the Illumina Human 1M Beadchip array, we identify 1,174 CNV loci in these populations that corroborated with findings when the same samples were typed on the Affymetrix 6.0 platform. We identify 441 novel loci not previously reported in the Database of Genomic Variations (DGV). We observe a considerable number of loci that span all three populations and were previously unreported, as well as population-specific loci that are quite common in the respective populations. From this we observe the distribution of CNVs in the Asian Indian population to be considerably different from the Chinese and Malay populations. About half of the deletion loci and three-quarters of duplication loci overlap UCSC genes. Tens of loci show population differentiation and overlap with genes previously known to be associated with genetic risk of diseases. One of these loci is the CYP2A6 deletion, previously linked to reduced susceptibility to lung cancer. (c) 2010 Wiley-Liss, Inc.

Use of Mobile Device Data To Better Estimate Dynamic Population Size for Wastewater-Based Epidemiology.

PubMed

Thomas, Kevin V; Amador, Arturo; Baz-Lomba, Jose Antonio; Reid, Malcolm

2017-10-03

Wastewater-based epidemiology is an established approach for quantifying community drug use and has recently been applied to estimate population exposure to contaminants such as pesticides and phthalate plasticizers. A major source of uncertainty in the population weighted biomarker loads generated is related to estimating the number of people present in a sewer catchment at the time of sample collection. Here, the population quantified from mobile device-based population activity patterns was used to provide dynamic population normalized loads of illicit drugs and pharmaceuticals during a known period of high net fluctuation in the catchment population. Mobile device-based population activity patterns have for the first time quantified the high degree of intraday, week, and month variability within a specific sewer catchment. Dynamic population normalization showed that per capita pharmaceutical use remained unchanged during the period when static normalization would have indicated an average reduction of up to 31%. Per capita illicit drug use increased significantly during the monitoring period, an observation that was only possible to measure using dynamic population normalization. The study quantitatively confirms previous assessments that population estimates can account for uncertainties of up to 55% in static normalized data. Mobile device-based population activity patterns allow for dynamic normalization that yields much improved temporal and spatial trend analysis.

Genetic differentiation among North Atlantic killer whale populations.

PubMed

Foote, Andrew D; Vilstrup, Julia T; De Stephanis, Renaud; Verborgh, Philippe; Abel Nielsen, Sandra C; Deaville, Robert; Kleivane, Lars; Martín, Vidal; Miller, Patrick J O; Oien, Nils; Pérez-Gil, Monica; Rasmussen, Morten; Reid, Robert J; Robertson, Kelly M; Rogan, Emer; Similä, Tiu; Tejedor, Maria L; Vester, Heike; Víkingsson, Gísli A; Willerslev, Eske; Gilbert, M Thomas P; Piertney, Stuart B

2011-02-01

Population genetic structure of North Atlantic killer whale samples was resolved from differences in allele frequencies of 17 microsatellite loci, mtDNA control region haplotype frequencies and for a subset of samples, using complete mitogenome sequences. Three significantly differentiated populations were identified. Differentiation based on microsatellite allele frequencies was greater between the two allopatric populations than between the two pairs of partially sympatric populations. Spatial clustering of individuals within each of these populations overlaps with the distribution of particular prey resources: herring, mackerel and tuna, which each population has been seen predating. Phylogenetic analyses using complete mitogenomes suggested two populations could have resulted from single founding events and subsequent matrilineal expansion. The third population, which was sampled at lower latitudes and lower density, consisted of maternal lineages from three highly divergent clades. Pairwise population differentiation was greater for estimates based on mtDNA control region haplotype frequencies than for estimates based on microsatellite allele frequencies, and there were no mitogenome haplotypes shared among populations. This suggests low or no female migration and that gene flow was primarily male mediated when populations spatially and temporally overlap. These results demonstrate that genetic differentiation can arise through resource specialization in the absence of physical barriers to gene flow. © 2010 Blackwell Publishing Ltd.

SSR characterization of Oryza glumaepatula populations from the Brazilian Amazon and Cerrado biomes.

PubMed

Abreu, Aluana Gonçalves; Rosa, Thalita Marra; Borba, Tereza Cristina de Oliveira; Vianello, Rosana Pereira; Rangel, Paulo Hideo Nakano; Brondani, Claudio

2015-08-01

The level and distribution of the genetic variability in 18 natural populations of Oryza glumaepatula that were collected from two Brazilian states were estimated using a set of 23 highly informative SSR markers. Samples comprising 78 and 117 individuals from populations of the states of Tocantins and Roraima, respectively, were evaluated in order to integrate and support previous studies that were carried out with populations of O. glumaepatula from Brazil. A total of 189 alleles were identified with an average of 8.22 alleles per locus. The 11 populations from Roraima presented, in combination, a higher genetic diversity (HE = 0.245) compared with that of the seven populations from Tocantins (HE = 0.212). All of the populations showed high and significant inbreeding values (mean f = 0.59); however, the mean was higher in Tocantins populations, indicating a higher gene flow in Roraima populations. The overall coefficient of genetic differentiation (FST) among the populations was high and significant (0.59) and was higher in Tocantins due to the isolation of each population, in contrast to Roraima, where gene flow occurred more frequently. The SSR panel used in this work resulted to be informative (polymorphism information content = 0.201) for assessing genetic structure in O. glumaepatula populations.

Overcoming the dichotomy between open and isolated populations using genomic data from a large European dataset

PubMed Central

Anagnostou, Paolo; Dominici, Valentina; Battaggia, Cinzia; Pagani, Luca; Vilar, Miguel; Wells, R. Spencer; Pettener, Davide; Sarno, Stefania; Boattini, Alessio; Francalacci, Paolo; Colonna, Vincenza; Vona, Giuseppe; Calò, Carla; Destro Bisol, Giovanni; Tofanelli, Sergio

2017-01-01

Human populations are often dichotomized into “isolated” and “open” categories using cultural and/or geographical barriers to gene flow as differential criteria. Although widespread, the use of these alternative categories could obscure further heterogeneity due to inter-population differences in effective size, growth rate, and timing or amount of gene flow. We compared intra and inter-population variation measures combining novel and literature data relative to 87,818 autosomal SNPs in 14 open populations and 10 geographic and/or linguistic European isolates. Patterns of intra-population diversity were found to vary considerably more among isolates, probably due to differential levels of drift and inbreeding. The relatively large effective size estimated for some population isolates challenges the generalized view that they originate from small founding groups. Principal component scores based on measures of intra-population variation of isolated and open populations were found to be distributed along a continuum, with an area of intersection between the two groups. Patterns of inter-population diversity were even closer, as we were able to detect some differences between population groups only for a few multidimensional scaling dimensions. Therefore, different lines of evidence suggest that dichotomizing human populations into open and isolated groups fails to capture the actual relations among their genomic features. PMID:28145502

Developing a general conceptual framework for avian conservation science

USGS Publications Warehouse

Sauer, J.R.

2003-01-01

Avian conservation science in North America has produced a variety of monitoring programs designed to provide information on population status of birds. Waterfowl surveys provide population estimates for breeding ducks over most of the continent, the North American Breeding Bird Survey (BBS) provides indexes to population change for >400 breeding bird species, and many other surveys exist that index bird populations at a variety of scales and seasons. However, many fundamental questions about bird population change remain unanswered. I suggest that analyses of monitoring data provide limited understanding of causes of population change, and that the declining species paradigm (Caughley 1994) is sometimes an inefficient approach to increasing our understanding of causes of population change. In North America, the North American Bird Conservation Initiative (NABCI) provides an opportunity to implement alternative approaches that use management, modeling of population responses to management, and monitoring in combination to increase our understanding of bird populations. In adaptive resources management, modeling provides predictions about consequences of management, and monitoring data allow us to assess the population consequences of management. In this framework, alternative hypotheses about response of populations to management can be evaluated by formulating a series of models with differing structure, and management and monitoring provide information about which model best predicts population response.

Comparisons of genetic diversity in captive versus wild populations of the federally endangered Quino checkerspot butterfly (Euphydryas editha quino Behr; Lepidoptera: Nymphalidae)

USGS Publications Warehouse

Miller, Mark P.; Pratt, Gordon F.; Mullins, Thomas D.; Haig, Susan M.

2014-01-01

Captive populations can play a significant role in threatened and endangered species management. An important consideration when developing and managing captive populations, however, is the maintenance of genetic diversity to ensure that adequate variation exists to avoid the negative consequences of inbreeding. In this investigation, we compared genetic diversity patterns within captive and wild populations of the federally endangered Quino checkerspot butterfly (Euphydryas editha quino Behr [Lepidoptera: Nymphalidae]), a taxon with a restricted distribution to chaparral and sage shrublands within Riverside and San Diego counties, California. Our analyses revealed that medium to high-frequency alleles from the wild populations were also present in the captive populations. While there was no significant difference in genetic diversity as quantified by expected heterozygosity, the captive populations showed tendencies toward significantly lower allelic richness than their wild counterparts. Given that alleles from the wild populations were occasionally not detected in captive populations, periodic incorporation of new wild specimens into the captive population would help ensure that allelic diversity is maintained to the extent possible. If performed in advance, genetic surveys of wild populations may provide the clearest insights regarding the number of individuals needed in captivity to adequately reflect wild populations.

Phenotypic diversity, population structure and stress protein-based capacitoring in populations of Xeropicta derbentina, a heat-tolerant land snail species.

PubMed

Di Lellis, Maddalena A; Sereda, Sergej; Geißler, Anna; Picot, Adrien; Arnold, Petra; Lang, Stefanie; Troschinski, Sandra; Dieterich, Andreas; Hauffe, Torsten; Capowiez, Yvan; Mazzia, Christophe; Knigge, Thomas; Monsinjon, Tiphaine; Krais, Stefanie; Wilke, Thomas; Triebskorn, Rita; Köhler, Heinz-R

2014-11-01

The shell colour of many pulmonate land snail species is highly diverse. Besides a genetic basis, environmentally triggered epigenetic mechanisms including stress proteins as evolutionary capacitors are thought to influence such phenotypic diversity. In this study, we investigated the relationship of stress protein (Hsp70) levels with temperature stress tolerance, population structure and phenotypic diversity within and among different populations of a xerophilic Mediterranean snail species (Xeropicta derbentina). Hsp70 levels varied considerably among populations, and were significantly associated with shell colour diversity: individuals in populations exhibiting low diversity expressed higher Hsp70 levels both constitutively and under heat stress than those of phenotypically diverse populations. In contrast, population structure (cytochrome c oxidase subunit I gene) did not correlate with phenotypic diversity. However, genetic parameters (both within and among population differences) were able to explain variation in Hsp70 induction at elevated but non-pathologic temperatures. Our observation that (1) population structure had a high explanatory potential for Hsp70 induction and that (2) Hsp70 levels, in turn, correlated with phenotypic diversity while (3) population structure and phenotypic diversity failed to correlate provides empirical evidence for Hsp70 to act as a mediator between genotypic variation and phenotype and thus for chaperone-driven evolutionary capacitance in natural populations.

A population on the rise: The origin of deepwater sculpin in Lake Ontario

USGS Publications Warehouse

Welsh, Amy B.; Scribner, Kim T.; Stott, Wendylee; Walsh, Maureen

2017-01-01

Deepwater sculpin, Myoxocephalus thompsonii, were thought to have been extirpated from Lake Ontario. However, in recent years, abundance has increased and recruitment has been documented. There are two hypotheses concerning the origin of the current Lake Ontario deepwater sculpin population. First, individuals from the upper Great Lakes may have recolonized Lake Ontario. Alternatively, the Lake Ontario population may have not been extirpated, and the remnant population has recovered naturally. To test these hypotheses, eight microsatellite loci were used to analyze samples from the current Lake Ontario population, museum specimens from the historic Lake Ontario population, and current upper Great Lakes populations. The genetic data suggest that historically throughout the Great Lakes, deepwater sculpin exhibited low levels of spatial genetic structure. Approximate Bayesian Computation analyses support the hypothesis that the current Lake Ontario population is more closely related to populations in the upper Great Lakes than to the historic Lake Ontario samples, indicating that the current Lake Ontario population likely resulted from recolonization from the Upper Great Lakes. The current Lake Ontario population has reduced allelic diversity relative to upper Great Lakes populations, indicating a possible founder effect. This study demonstrates the role life history variation can play in recolonization success. The pelagic larval phase of the deepwater sculpin allowed recolonization of Lake Ontario via passive larval drift.

Genetic variation of Sargassum horneri populations detected by inter-simple sequence repeats.

PubMed

Ren, J R; Yang, R; He, Y Y; Sun, Q H

2015-01-30

The seaweed Sargassum horneri is an important brown alga in the marine environment, and it is an important raw material in the alginate industry. Unfortunately, the fixed resource that was originally reported is now reduced or disappeared, and increased floating populations have been reported in recent years. We sampled a floating population and 4 fixed cultivated populations of S. horneri along the coast of Zhejiang, China. Inter-simple sequence repeat (ISSR) markers were applied in this research to analyze the genetic variation between floating populations and fixed cultivated populations of S. horneri. In total, 220 loci were amplified with 23 ISSR primers. The percentage of polymorphic loci within each population ranged from 53.64 to 95.45%. The highest diversity was observed in population 3, which was the local species that was suspension cultured in the lab and then fixed cultivated in the Nanji Islands before sampling. The lowest diversity was obtained in the floating population 4. The genetic distances among the 5 S. horneri populations ranged from 0.0819 to 0.2889, and the distance tendency confirmed the genetic diversity. The results suggest that the floating population had the lowest genetic diversity and could not be joined into the cluster branch of the fixed cultivated populations.

Population genetics and the evolution of geographic range limits in an annual plant.

PubMed

Moeller, David A; Geber, Monica A; Tiffin, Peter

2011-10-01

Abstract Theoretical models of species' geographic range limits have identified both demographic and evolutionary mechanisms that prevent range expansion. Stable range limits have been paradoxical for evolutionary biologists because they represent locations where populations chronically fail to respond to selection. Distinguishing among the proposed causes of species' range limits requires insight into both current and historical population dynamics. The tools of molecular population genetics provide a window into the stability of range limits, historical demography, and rates of gene flow. Here we evaluate alternative range limit models using a multilocus data set based on DNA sequences and microsatellites along with field demographic data from the annual plant Clarkia xantiana ssp. xantiana. Our data suggest that central and peripheral populations have very large historical and current effective population sizes and that there is little evidence for population size changes or bottlenecks associated with colonization in peripheral populations. Whereas range limit populations appear to have been stable, central populations exhibit a signature of population expansion and have contributed asymmetrically to the genetic diversity of peripheral populations via migration. Overall, our results discount strictly demographic models of range limits and more strongly support evolutionary genetic models of range limits, where adaptation is prevented by a lack of genetic variation or maladaptive gene flow.

The world population explosion: causes, backgrounds and projections for the future

PubMed Central

Van Bavel, J.

2013-01-01

At the beginning of the nineteenth century, the total world population crossed the threshold of 1 billion people for the first time in the history of the homo sapiens sapiens. Since then, growth rates have been increasing exponentially, reaching staggeringly high peaks in the 20th century and slowing down a bit thereafter. Total world population reached 7 billion just after 2010 and is expected to count 9 billion by 2045. This paper first charts the differences in population growth between the world regions. Next, the mechanisms behind unprecedented population growth are explained and plausible scenarios for future developments are discussed. Crucial for the long term trend will be the rate of decline of the number of births per woman, called total fertility. Improvements in education, reproductive health and child survival will be needed to speed up the decline of total fertility, particularly in Africa. But in all scenarios, world population will continue to grow for some time due to population momentum. Finally, the paper outlines the debate about the consequences of the population explosion, involving poverty and food security, the impact on the natural environment, and migration flows. Key words: Fertility, family planning, world population, population growth, demographic transition, urbanization, population momentum, population projections. PMID:24753956

Using population genetic tools to develop a control strategy for feral cats (Felis catus) in Hawai'i

USGS Publications Warehouse

Hansen, H.; Hess, S.C.; Cole, D.; Banko, P.C.

2007-01-01

Population genetics can provide information about the demographics and dynamics of invasive species that is beneficial for developing effective control strategies. We studied the population genetics of feral cats on Hawai'i Island by microsatellite analysis to evaluate genetic diversity and population structure, assess gene flow and connectivity among three populations, identify potential source populations, characterise population dynamics, and evaluate sex-biased dispersal. High genetic diversity, low structure, and high number of migrants per generation supported high gene flow that was not limited spatially. Migration rates revealed that most migration occurred out of West Mauna Kea. Effective population size estimates indicated increasing cat populations despite control efforts. Despite high gene flow, relatedness estimates declined significantly with increased geographic distance and Bayesian assignment tests revealed the presence of three population clusters. Genetic structure and relatedness estimates indicated male-biased dispersal, primarily from Mauna Kea, suggesting that this population should be targeted for control. However, recolonisation seems likely, given the great dispersal ability that may not be inhibited by barriers such as lava flows. Genetic monitoring will be necessary to assess the effectiveness of future control efforts. Management of other invasive species may benefit by employing these population genetic tools. ?? CSIRO 2007.

Stable, semi-stable populations and growth potential.

PubMed

Bourgeois-Pichat, J

1971-07-01

Abstract Starting from the definition of a Malthusian population given by Alfred J. Lotka, the author recalls how the concept of stable population is introduced in demography, first as a particular case of stable populations, and secondly as a limit of a demographic evolutionary process in which female age-specific fertility rates and age-specific mortality rates remain constant. Then he defines a new concept: the semi-stable population which is a population with a constant age distribution. He shows that such a population coincides at any point of time with the stable population corresponding to the mortality and the fertility at this point of time. In the remaining part of the paper it is shown how the concept of a stable population can be used for defining a coefficient of inertia which measures the resistance of a population to modification of its course as a consequence of changing fertility and mortality. Some formulae are established to calculate this coefficient first for an arbitrary population, and secondly for a semistable population. In this second case the formula is particularly simple. It appears as a product of three terms: the expectation of life at birth in years, the crude birth rate, and a coefficient depending on the rate of growth and for which a numerical table is easy to establish.

Genome-wide signatures of population bottlenecks and diversifying selection in European wolves

PubMed Central

Pilot, M; Greco, C; vonHoldt, B M; Jędrzejewska, B; Randi, E; Jędrzejewski, W; Sidorovich, V E; Ostrander, E A; Wayne, R K

2014-01-01

Genomic resources developed for domesticated species provide powerful tools for studying the evolutionary history of their wild relatives. Here we use 61K single-nucleotide polymorphisms (SNPs) evenly spaced throughout the canine nuclear genome to analyse evolutionary relationships among the three largest European populations of grey wolves in comparison with other populations worldwide, and investigate genome-wide effects of demographic bottlenecks and signatures of selection. European wolves have a discontinuous range, with large and connected populations in Eastern Europe and relatively smaller, isolated populations in Italy and the Iberian Peninsula. Our results suggest a continuous decline in wolf numbers in Europe since the Late Pleistocene, and long-term isolation and bottlenecks in the Italian and Iberian populations following their divergence from the Eastern European population. The Italian and Iberian populations have low genetic variability and high linkage disequilibrium, but relatively few autozygous segments across the genome. This last characteristic clearly distinguishes them from populations that underwent recent drastic demographic declines or founder events, and implies long-term bottlenecks in these two populations. Although genetic drift due to spatial isolation and bottlenecks seems to be a major evolutionary force diversifying the European populations, we detected 35 loci that are putatively under diversifying selection. Two of these loci flank the canine platelet-derived growth factor gene, which affects bone growth and may influence differences in body size between wolf populations. This study demonstrates the power of population genomics for identifying genetic signals of demographic bottlenecks and detecting signatures of directional selection in bottlenecked populations, despite their low background variability. PMID:24346500