[Study on VNTR diversity of clinical Mycobacterium tuberculosis isolates from Qinghai].

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Li, Bin; Liu, Haican; Wang, Zhaofen; Ma, Yongcheng; Su, Xiaodong; Jiang, Mingxia; Wan, Kanglin; Liu, Shou; Zhao, Xiuqin; Qu, Shugen

2015-10-01

To investigate the variable number tandem repeats (VNTR) genetic polymorphisms, genotyping and distribution pattern of clinical Mycobacterium (M.) tuberculosis isolates from Qinghai province. The clinical M. tuberculosis strains isolated from the patients with tuberculosis and related background data were collected from Qinghai Provincial Center for Disease Control and Prevention from 2009 to 2012. Genotyping was conducted by using multiple locus VNTR analysis (MLVA). Genomic DNA was extracted and 15 VNTR loci were amplified with PCR and the PCR products were detected with gel electrophoresis. The VNTR diversity and clusters of genotyping were analyzed with BioNumerics (Version 5.0). A total of 251 clinical M. tuberculosis isolates were analyzed with 15 VNTR loci showing that there were great genetic diversity in these isolates. Six of the 15 VNTR loci, showed that the Hunter-Gaston index (HGI) were higher than 0.6, in which the highest resolution was MIRU26. The clusters of genotyping showed that these isolates could be categorized into four gene clusters and 238 genotypes. The four gene clusters accounted for 4.9%, 91.9%, 1.6% and 1.6% of the clinical isolates, respectively. The results showed that there is great variety of VNTR genetic polymorphisms in clinical M. tuberculosis isolates in Qinghai province.

Genetic diversity of perch rhabdoviruses isolates based on the nucleoprotein and glycoprotein genes.

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Talbi, Chiraz; Cabon, Joelle; Baud, Marine; Bourjaily, Maya; de Boisséson, Claire; Castric, Jeannette; Bigarré, Laurent

2011-12-01

Despite the increasing impact of rhabdoviruses in European percid farming, the diversity of the viral populations is still poorly investigated. To address this issue, we sequenced the partial nucleoprotein (N) and complete glycoprotein (G) genes of nine rhabdoviruses isolated from perch (Perca fluviatilis) between 1999 and 2010, mostly from France, and analyzed six of them by immunofluorescence antibody test (IFAT). Using two rabbit antisera raised against either the reference perch rhabdovirus (PRhV) isolated in 1980 or the perch isolate R6146, two serogroups were distinguished. Meanwhile, based on partial N and complete G gene analysis, perch rhabdoviruses were divided into four genogroups, A-B-D and E, with a maximum of 32.9% divergence (G gene) between isolates. A comparison of the G amino acid sequences of isolates from the two identified serogroups revealed several variable regions that might account for antigenic differences. Comparative analysis of perch isolates with other rhabdoviruses isolated from black bass, pike-perch and pike showed some strong phylogenetic relationships, suggesting cross-host transmission. Similarly, striking genetic similarities were shown between perch rhabdoviruses and isolates from other European countries and various ecological niches, most likely reflecting the circulation of viruses through fish trade as well as putative transfers from marine to freshwater fish. Phylogenetic relationships of the newly characterized viruses were also determined within the family Rhabdoviridae. The analysis revealed a genetic cluster containing only fish viruses, including all rhabdoviruses from perch, as well as siniperca chuatsi rhabdovirus (SCRV) and eel virus X (EVEX). This cluster was distinct from the one represented by spring viraemia of carp vesiculovirus (SVCV), pike fry rhabdovirus (PFRV) and mammalian vesiculoviruses. The new genetic data provided in the present study shed light on the diversity of rhabdoviruses infecting perch in

Genetic diversity and antifungal susceptibility of Fusarium isolates in onychomycosis.

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Rosa, Priscila D; Heidrich, Daiane; Corrêa, Carolina; Scroferneker, Maria Lúcia; Vettorato, Gerson; Fuentefria, Alexandre M; Goldani, Luciano Z

2017-09-01

Fusarium species have emerged as an important human pathogen in skin disease, onychomycosis, keratitis and invasive disease. Onychomycosis caused by Fusarium spp. The infection has been increasingly described in the immunocompetent and immunosuppressed hosts. Considering onychomycosis is a difficult to treat infection, and little is known about the genetic variability and susceptibility pattern of Fusarium spp., further studies are necessary to understand the pathogenesis and better to define the appropriate antifungal treatment for this infection. Accordingly, the objective of this study was to describe the in vitro susceptibility to different antifungal agents and the genetic diversity of 35 Fusarium isolated from patients with onychomycosis. Fusarium spp. were isolated predominantly from female Caucasians, and the most frequent anatomical location was the nail of the hallux. Results revealed that 25 (71.4%) of isolates belonged to the Fusarium solani species complex, followed by 10 (28.5%) isolates from the Fusarium oxysporum species complex. Noteworthy, the authors report the first case of Neocosmospora rubicola isolated from a patient with onychomycosis. Amphotericin B was the most effective antifungal agent against the majority of isolates (60%, MIC ≤4 μg/mL), followed by voriconazole (34.2%, MIC ≤4 μg/mL). In general, Fusarium species presented MIC values >64 μg/mL for fluconazole, itraconazole and terbinafine. Accurate pathogen identification, characterisation and susceptibility testing provide a better understanding of pathogenesis of Fusarium in onychomycosis. © 2017 Blackwell Verlag GmbH.

Isolation of Geobacter species from diverse sedimentary environments

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Coaxes, J.D.; Phillips, E.J.P.; Lonergan, D.J.; Jenter, H.; Lovley, D.R.

1996-01-01

In an attempt to better understand the microorganisms responsible for Fe(III) reduction in sedimentary environments, Fe(III)-reducing microorganisms were enriched for and isolated from freshwater aquatic sediments, a pristine deep aquifer, and a petroleum-contaminated shallow aquifer. Enrichments were initiated with acetate or toluene as the electron donor and Fe(III) as the electron acceptor. Isolations were made with acetate or benzoate. Five new strains which could obtain energy for growth by dissimilatory Fe(III) reduction were isolated. All five isolates are gram- negative strict anaerobes which grow with acetate as the electron donor and Fe(III) as the electron acceptor. Analysis of the 16S rRNA sequence of the isolated organisms demonstrated that they all belonged to the genus Geobacter in the delta subdivision of the Proteobacteria. Unlike the type strain, Geobacter metallireducens, three of the five isolates could use H2 as an electron donor fur Fe(III) reduction. The deep subsurface isolate is the first Fe(III) reducer shown to completely oxidize lactate to carbon dioxide, while one of the freshwater sediment isolates is only the second Fe(III) reducer known that can oxidize toluene. The isolation of these organisms demonstrates that Geobacter species are widely distributed in a diversity of sedimentary environments in which Fe(III) reduction is an important process.

Characterization of sequence diversity in Plasmodium falciparum SERA5 from Indian isolates

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Rahul C.N

2015-06-01

Full Text Available Objective: To characterize the sequence diversity of blood-stage Plasmodium falciparum serine repeat antigen-5 (PfSERA5 which is lacking in a malaria-endemic country like India. Methods: In this study, parasitic DNA was obtained from field isolates collected from various geographic regions. Subsequently, PfSERA5 gene sequence was PCR amplified and DNA sequenced. Results: We reported the existence of unique repeat polymorphisms and novel haplotypes for both the octamer repeat (OR and serine repeat (SR regions of the N-terminal fragment of PfSERA5 from Indian isolates. Several isolates from India were identical to low-frequency African haplotypes. Unique finding of our study was an Indian isolate showing deletion in a perfectly conserved 14 mer sequence within octamer repeat. Indian haplotypes reported in this study were found to be distributed into the three earlier classified allelic clusters of FCR3, K1 and Honduras showcasing broad diversity as compared to worldwide haplotypes. Conclusions: This study is the first report on genetic diversity of PfSERA5 antigen from India. Further evaluation of these haplotypes by serotyping would provide useful information for investigating variant-specific immunity and aid in malaria vaccine research.

Genetic diversity of Actinobacillus lignieresii isolates from different hosts

DEFF Research Database (Denmark)

Kokotovic, Branko; Angen, Øystein; Bisgaard, Magne

2011-01-01

Genetic diversity detected by analysis of amplified fragment length polymorphisms (AFLPs) of 54 Actinobacilus lignieresii isolates from different hosts and geographic localities is described. On the basis of variances in AFLP profiles, the strains were grouped in two major clusters; one comprisin...

Diversity of Geotrichum candidum strains isolated from traditional cheesemaking fabrications in France.

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Marcellino, N; Beuvier, E; Grappin, R; Guéguen, M; Benson, D R

2001-10-01

The diversity of French fungus-ripened cheeses is due partly to the succession of fungi that colonize the cheese during ripening. Geotrichum candidum appears in the early stages of ripening on soft cheeses such as Camembert and semihard cheeses such as St. Nectaire and Reblochon. Its lipases and proteases promote flavor development, and its aminopeptidases reduce bitterness imparted by low-molecular-weight peptides in cheese. We assessed the genetic diversity of G. candidum strains by using random amplification of polymorphic DNA (RAPD)-PCR correlated with phenotypic tests for carbon assimilation and salt tolerance. Strains were isolated from milk, curd, and cheese collected in seven major cheesemaking regions of France. Sixty-four isolates were characterized. We found high genetic diversity of G. candidum even within the same cheesemaking regions. Strains did not group according to region. All of the strains from the Haute-Savoie were able to assimilate lactate as the sole source of carbon, while lactate assimilation varied among strains from the Auvergne. Strains varied in D-mannitol assimilation, and none used citrate as the sole source of carbon. Yeast-like colony morphology predominated in Reblochon, while all of the strains isolated from St. Nectaire were filamentous. The RAPD-PCR technique readily differentiated Geotrichum fragrans isolated from milk and curd in a St. Nectaire cheesemaking facility. This study reveals an enormous diversity of G. candidum that has been empirically selected through the centuries by the cheesemakers of France.

Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis.

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Jun, Se-Ran; Wassenaar, Trudy M; Nookaew, Intawat; Hauser, Loren; Wanchai, Visanu; Land, Miriam; Timm, Collin M; Lu, Tse-Yuan S; Schadt, Christopher W; Doktycz, Mitchel J; Pelletier, Dale A; Ussery, David W

2016-01-01

The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity and heterogeneity of these communities. On the basis of average amino acid identity, comparative genome analysis of >1,000 Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides (eastern cottonwood) trees resulted in consistent and robust genomic clusters with phylogenetic homogeneity. All Pseudomonas aeruginosa genomes clustered together, and these were clearly distinct from other Pseudomonas species groups on the basis of pangenome and core genome analyses. In contrast, the genomes of Pseudomonas fluorescens were organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. Most of our 21 Populus-associated isolates formed three distinct subgroups within the major P. fluorescens group, supported by pathway profile analysis, while two isolates were more closely related to Pseudomonas chlororaphis and Pseudomonas putida. Genes specific to Populus-associated subgroups were identified. Genes specific to subgroup 1 include several sensory systems that act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor. Genes specific to subgroup 2 contain hypothetical genes, and genes specific to subgroup 3 were annotated with hydrolase activity. This study justifies the need to sequence multiple isolates, especially from P. fluorescens, which displays the most genetic variation, in order to study functional capabilities from a pangenomic perspective. This information will prove useful when choosing Pseudomonas strains for use to promote growth and increase disease resistance in plants. Copyright © 2015 Jun et al.

CPm gene diversity in field isolates of Citrus tristeza virus from Colombia.

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Oliveros-Garay, Oscar Arturo; Martinez-Salazar, Natalhie; Torres-Ruiz, Yanneth; Acosta, Orlando

2009-01-01

The nucleotide sequence diversity of the CPm gene from 28 field isolates of Citrus tristeza virus (CTV) was assessed by SSCP and sequence analyses. These isolates showed two major shared haplotypes, which differed in distribution: A1 was the major haplotype in 23 isolates from different geographic regions, whereas R1 was found in isolates from a discrete region. Phylogenetic reconstruction clustered A1 within an independent group, while R1 was grouped with mild isolates T30 from Florida and T385 from Spain. Some isolates contained several minor haplotypes, which were very similar to, and associated with, the major haplotype.

Diversity of thermophilic archaeal isolates from hot springs in Japan

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Itoh, Takashi; Yoshikawa, Naoto; Takashina, Tomonori

2005-09-01

In the light of the significance of extremophiles as model organisms to access possible extraterrestiral life, we provide a short review of the systematics of thermophilic Archaea, and introduce our exploratory research of novel thermophilic Archaea from hot springs in Japan. Up to date, we have isolated 162 strains of the thermophilic Archaea from hot springs in Japan by the enrichment method or the most probable number/PCR method, and the 16S rRNA gene sequences were determined to reveal their phylogenetic diversity. The sequence comparison illustrated that the isolates belonged to the orders Sulfolobales (117 isolates) , Thermoproteales (29 isolates), Desulfurococcales (8 isolates) and Thermoplasmatales (8 isolates), and there were six separate lineages representing new genera, and at least seven new species as predicted by the phylogenetic distance to known species. The collection of isolates not only included novel taxa but would give some implication for a necessity to reevaluate the current taxonomy of the thermophilic Archaea.

Phylogenetic diversity and biological activity of culturable Actinobacteria isolated from freshwater fish gut microbiota.

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Jami, Mansooreh; Ghanbari, Mahdi; Kneifel, Wolfgang; Domig, Konrad J

2015-06-01

The diversity of Actinobacteria isolated from the gut microbiota of two freshwater fish species namely Schizothorax zarudnyi and Schizocypris altidorsalis was investigated employing classical cultivation techniques, repetitive sequence-based PCR (rep-PCR), partial and full 16S rDNA sequencing followed by phylogenetic analysis. A total of 277 isolates were cultured by applying three different agar media. Based on rep-PCR profile analysis a subset of 33 strains was selected for further phylogenetic investigations, antimicrobial activity testing and diversity analysis of secondary-metabolite biosynthetic genes. The identification based on 16S rRNA gene sequencing revealed that the isolates belong to eight genera distributed among six families. At the family level, 72% of the 277 isolates belong to the family Streptomycetaceae. Among the non-streptomycetes group, the most dominant group could be allocated to the family of Pseudonocardiaceae followed by the members of Micromonosporaceae. Phylogenetic analysis clearly showed that many of the isolates in the genera Streptomyces, Saccharomonospora, Micromonospora, Nocardiopsis, Arthrobacter, Kocuria, Microbacterium and Agromyces formed a single and distinct cluster with the type strains. Notably, there is no report so far about the occurrence of these Actinobacteria in the microbiota of freshwater fish. Of the 33 isolates, all the strains exhibited antibacterial activity against a set of tested human and fish pathogenic bacteria. Then, to study their associated potential capacity to synthesize diverse bioactive natural products, diversity of genes associated with secondary-metabolite biosynthesis including PKS I, PKS II, NRPS, the enzyme PhzE of the phenazine pathways, the enzyme dTGD of 6-deoxyhexoses glycosylation pathway, the enzyme Halo of halogenation pathway and the enzyme CYP in polyene polyketide biosynthesis were investigated among the isolates. All the strains possess at least two types of the investigated

Mycobacterium tuberculosis Isolates from Single Outpatient Clinic in Panama City Exhibit Wide Genetic Diversity

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Sambrano, Dilcia; Correa, Ricardo; Almengor, Pedro; Domínguez, Amada; Vega, Silvio; Goodridge, Amador

2014-01-01

Understanding Mycobacterium tuberculosis biodiversity and transmission is significant for tuberculosis control. This short report aimed to determine the genetic diversity of M. tuberculosis isolates from an outpatient clinic in Panama City. A total of 62 M. tuberculosis isolates were genotyped by 12 loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and Spoligotyping. Forty-five (72.6%) of the isolates showed unique MIRU-VNTR genotypes, and 13 (21%) of the isolates were grouped into four clusters. Four isolates showed polyclonal MIRU-VNTR genotypes. The MIRU-VNTR Hunter-Gaston discriminatory index reached 0.988. The Spoligotyping analysis revealed 16 M. tuberculosis families, including Latin American-Mediterranean, Harlem, and Beijing. These findings suggest a wide genetic diversity of M. tuberculosis isolates at one outpatient clinic. A detailed molecular epidemiology survey is now warranted, especially following second massive immigration for local Panama Canal expansion activities. PMID:24865686

Genetic Diversity Among Colletotrichum falcatum Isolates Causing Red Rot of Sugarcane in Subtropical Region of India

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Ratinderbir KAUR

2014-09-01

Full Text Available Silver Genetic diversity of Colletotrichum falcatum causing red rot of sugarcane was assessed based on morphological, pathological and molecular characteristics especially from sub-tropical Indian conditions. Sixteen isolates of this pathogen were collected based on the extensive survey on prominent varieties grown in the region along with some elite selections. Morphological observations (colony colour, mycelium pattern and sporulation grouped the isolates into two distinct types (C1: light type and C2: dark type. However, quantitative data on colony diameter showed five clusters for these isolates. Pathogenic characterization of these isolates on fourteen standard differentials formed six groups, ingroup 1: (CF-Pb-1 isolates Cf-157, Cf-249 and Cf-248 were the most virulent while group 6 (CF-Pb-6 isolates Cf-60 and Cf-247 were the least one. The genetic relatedness among the isolates using Random Amplified Polymorphic DNA (RAPD analysis revealed sufficient molecular polymorphism, which in turn confirmed the variation in virulence of different isolates. The data categorized different isolates into two major clusters and five independent lineages. Polymorphic information content (PIC ranged from 0.701 to 0.929. Isolate Cf-223 was found to be genetically most diverse among all the isolates. Present study inferred that morphological grouping of most of the isolates showed positive correlation with the pathogenic variability while molecular diversity did not showed such associations.

[Community structure and diversity of culturable moderate halophilic bacteria isolated from Qrhan salt lake on Qinghai-Tibet Plateau].

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Shen, Shuo

2017-04-04

I studied the community structure and diversity of culturable moderate halophilic bacteria isolated from Qrhan Salt Lake. I isolated and cultured the moderate halophilic bacteria on different selective media. After the 16S rRNA gene sequences was amplified and measured, I constructed the phylogenic tree, analyzed the community structure and calculated the diversity indexes according to the 16S rRNA gene information. A total of 421 moderate halophilic bacteria were isolated from water and mud samples in Qrhan Salt Lake. The 16S rRNA gene information showed that 4 potential novel species belonged to the family Bacillaceae. Eighty-three model strains belonged to 3 phylurms 6 families 16 genus. Among them, Bacillus sp., Oceanobacillus sp. and Halomonas sp. were dominant species. Diversity analysis showed that the diversity of strains isolated from water sample was higher than that from mud sample, but the dominance degree of strains isolated from mud sample was higher than that from water sample. The genetic diversity of moderate halophilic bacteria isolated from Qrhan Salt Lake was abundant. Also, there were dominant and novel species of culturable moderate halophilic bacteria in this lake.

Genetic diversity and virulence genes in Streptococcus uberis strains isolated from bovine mastitis

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Rafael Ambrósio Loures

2017-08-01

Full Text Available Mastitis is one of the most common and costly infectious diseases in dairy cattle worldwide. This is a multifactorial illness caused by different microorganisms, including virus, yeasts, algae, parasites, and several species of bacteria. Among these bacteria, Streptococcus uberis is an important environmental pathogen that is responsible for a large range of clinical and subclinical mammary infections, especially in intensively managed herds. Despite the increasing importance of this pathogen in the etiology of bovine mastitis, data on its virulence and diversity in Brazilian dairy herds are scarce. The aims of the present study were to investigate the virulence characteristics of S. uberis isolated from bovine mastitis and to assess the molecular epidemiology of the Brazilian isolates using pulsed-field gel electrophoresis (PFGE. In this work, 46 strains of S. uberis isolated from bovine mastitis from 26 Brazilian dairy herds were evaluated regarding their genetic diversity by PFGE using with the SmaI enzyme. Additionally, the presence of the virulence genes skc and pauA, which encode plasminogen activators, and the gene sua, which encodes an adhesion molecule in mammary epithelial cells, were assessed by PCR. Our results showed a high genetic diversity in the population, displaying many different patterns in the PFGE analysis. A high proportion of strains was positive for virulence genes in the sampled population (sua [100%], pauA [91%], and skc [91%]. The high frequency of skc, pauA, and sua genes among the studied strains suggests the importance of these virulence factors, possibly helping S. uberis in the colonization of the bovine mammary gland. Surveys of the genetic and molecular characteristics of this pathogen can improve our knowledge of bacterial activity and identify molecules that have roles in the establishment of the infection. This might help in the development of more effective measures to control and prevent bovine mastitis.

Diversity of Clostridium perfringens isolates from various sources and prevalence of conjugative plasmids.

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Park, Miseon; Deck, Joanna; Foley, Steven L; Nayak, Rajesh; Songer, J Glenn; Seibel, Janice R; Khan, Saeed A; Rooney, Alejandro P; Hecht, David W; Rafii, Fatemeh

2016-04-01

Clostridium perfringens is an important pathogen, causing food poisoning and other mild to severe infections in humans and animals. Some strains of C. perfringens contain conjugative plasmids, which may carry antimicrobial resistance and toxin genes. We studied genomic and plasmid diversity of 145 C. perfringens type A strains isolated from soils, foods, chickens, clinical samples, and domestic animals (porcine, bovine and canine), from different geographic areas in the United States between 1994 and 2006, using multiple-locus variable-number tandem repeat analysis (MLVA) and/or pulsed-field gel electrophoresis (PFGE). MLVA detected the genetic diversity in a majority of the isolates. PFGE, using SmaI and KspI, confirmed the MLVA results but also detected differences among the strains that could not be differentiated by MLVA. All of the PFGE profiles of the strains were different, except for a few of the epidemiologically related strains, which were identical. The PFGE profiles of strains isolated from the same domestic animal species were clustered more closely with each other than with other strains. However, a variety of C. perfringens strains with distinct genetic backgrounds were found among the clinical isolates. Variation was also observed in the size and number of plasmids in the strains. Primers for the internal fragment of a conjugative tcpH gene of C. perfringens plasmid pCPF4969 amplified identical size fragments from a majority of strains tested; and this gene hybridized to the various-sized plasmids of these strains. The sequences of the PCR-amplified tcpH genes from 12 strains showed diversity among the tcpH genes. Regardless of the sources of the isolates, the genetic diversity of C. perfringens extended to the plasmids carrying conjugative genes. Published by Elsevier Ltd.

Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing

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Pruckler James M

2008-11-01

Full Text Available Abstract Background Bacillus cereus is most commonly associated with foodborne illness (diarrheal and emetic but is also an opportunistic pathogen that can cause severe and fatal infections. Several multilocus sequence typing (MLST schemes have recently been developed to genotype B. cereus and analysis has suggested a clonal or weakly clonal population structure for B. cereus and its close relatives B. anthracis and B. thuringiensis. In this study we used MLST to determine if B. cereus isolates associated with illnesses of varying severity (e.g., severe, systemic vs. gastrointestinal (GI illness were clonal or formed clonal complexes. Results A retrospective analysis of 55 clinical B. cereus isolates submitted to the Centers for Disease Control and Prevention between 1954 and 2004 was conducted. Clinical isolates from severe infections (n = 27, gastrointestinal (GI illness (n = 18, and associated isolates from food (n = 10 were selected for analysis using MLST. The 55 isolates were diverse and comprised 38 sequence types (ST in two distinct clades. Of the 27 isolates associated with serious illness, 13 clustered in clade 1 while 14 were in clade 2. Isolates associated with GI illness were also found throughout clades 1 and 2, while no isolates in this study belonged to clade 3. All the isolates from this study belonging to the clade 1/cereus III lineage were associated with severe disease while isolates belonging to clade1/cereus II contained isolates primarily associated with severe disease and emetic illness. Only three STs were observed more than once for epidemiologically distinct isolates. Conclusion STs of clinical B. cereus isolates were phylogenetically diverse and distributed among two of three previously described clades. Greater numbers of strains will need to be analyzed to confirm if specific lineages or clonal complexes are more likely to contain clinical isolates or be associated with specific illness, similar to B. anthracis and

Diversity of DNA fingerprints of Mycobacterium tuberculosis isolates in the United States.

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Yang, Z; Barnes, P F; Chaves, F; Eisenach, K D; Weis, S E; Bates, J H; Cave, M D

1998-04-01

To investigate the diversity of IS6110 fingerprints of Mycobacterium tuberculosis isolates in the United States and to determine if matching IS6110 fingerprints represent recent interstate tuberculosis transmission, we performed restriction fragment length polymorphism analysis of M. tuberculosis isolates from 1,326 patients in three geographically separated states. Seven hundred ninety-five different IS6110 fingerprint patterns were generated, and pattern diversity was similar in each state. Ninety-six percent of the fingerprint patterns were observed in only one state, demonstrating that most IS6110 fingerprint patterns are confined to a single geographic location. Of the IS6110 fingerprint patterns that were shared by isolates from more than one state, most isolates with 1 to 5 IS6110 copies were separable by pTBN12 fingerprinting whereas those with > 15 copies were not. One high-copy-number M. tuberculosis strain had identical IS6110 and pTBN12 fingerprints and included 57 isolates from three states. Epidemiological data demonstrated significant recent transmission of tuberculosis within each city but not among the states. This suggests that identical fingerprints of isolates from geographically separate locations most likely reflect interstate tuberculosis transmission in the past, with subsequent intrastate spread of disease. Further evaluation of M. tuberculosis strains that cause outbreaks in different geographic locations will provide insight into the epidemiological and bacteriological factors that facilitate the spread of tuberculosis.

Optimal diversity: Increasing returns versus recombinant innovation

NARCIS (Netherlands)

van den Bergh, J.C.J.M.; Zeppini Rossi, P.

2008-01-01

Choices regarding diversity play an important role in economics and innovation management, but often remain implicit. Once made explicit, the objectives of efficiency and diversity are usually posed as in conflict, as efficiency relates positively and diversity negatively to various increasing

Plant diversity and regeneration in a disturbed isolated dry Afromontane forest in northern Ethiopia

DEFF Research Database (Denmark)

Aynekulu, Ermias; Aerts, Raf; Denich, Manfred

2016-01-01

We studied the diversity, community composition and natural regeneration of woody species in an isolated but relatively large (> 1,000 ha) dry Afromontane forest in northern Ethiopia to assess its importance for regional forest biodiversity conservation. The principal human-induced disturbance...... in biodiversity through local extinction of indigenous tree species. Despite the problems associated with conserving plant species diversity in small and isolated populations, this relic forest is of particular importance for regional conservation of forest biodiversity, as species with high conservation value...

Genomic diversity among Beijing and non-Beijing Mycobacterium tuberculosis isolates from Myanmar.

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Ruth Stavrum

2008-04-01

Full Text Available The Beijing family of Mycobacterium tuberculosis is dominant in countries in East Asia. Genomic polymorphisms are a source of diversity within the M. tuberculosis genome and may account for the variation of virulence among M. tuberculosis isolates. Till date there are no studies that have examined the genomic composition of M. tuberculosis isolates from the high TB-burden country, Myanmar.Twenty-two M. tuberculosis isolates from Myanmar were screened on whole-genome arrays containing genes from M. tuberculosis H37Rv, M. tuberculosis CDC1551 and M. bovis AF22197. Screening identified 198 deletions or extra regions in the clinical isolates compared to H37Rv. Twenty-two regions differentiated between Beijing and non-Beijing isolates and were verified by PCR on an additional 40 isolates. Six regions (Rv0071-0074 [RD105], Rv1572-1576c [RD149], Rv1585c-1587c [RD149], MT1798-Rv1755c [RD152], Rv1761c [RD152] and Rv0279c were deleted in Beijing isolates, of which 4 (Rv1572-1576c, Rv1585c-1587c, MT1798-Rv1755c and Rv1761c were variably deleted among ST42 isolates, indicating a closer relationship between the Beijing and ST42 lineages. The TbD1 region, Mb1582-Mb1583 was deleted in Beijing and ST42 isolates. One M. bovis gene of unknown function, Mb3184c was present in all isolates, except 11 of 13 ST42 isolates. The CDC1551 gene, MT1360 coding for a putative adenylate cyclase, was present in all Beijing and ST42 isolates (except 1. The pks15/1 gene, coding for a putative virulence factor, was intact in all Beijing and non-Beijing isolates, except in ST42 and ST53 isolates.This study describes previously unreported deletions/extra regions in Beijing and non-Beijing M. tuberculosis isolates. The modern and highly frequent ST42 lineage showed a closer relationship to the hypervirulent Beijing lineage than to the ancient non-Beijing lineages. The pks15/1 gene was disrupted only in modern non-Beijing isolates. This is the first report of an in-depth analysis on

Genetic diversity among Puccinia melanocephala isolates from Brazil assessed using simple sequence repeat markers.

Science.gov (United States)

Peixoto-Junior, R F; Creste, S; Landell, M G A; Nunes, D S; Sanguino, A; Campos, M F; Vencovsky, R; Tambarussi, E V; Figueira, A

2014-09-26

Brown rust (causal agent Puccinia melanocephala) is an important sugarcane disease that is responsible for large losses in yield worldwide. Despite its importance, little is known regarding the genetic diversity of this pathogen in the main Brazilian sugarcane cultivation areas. In this study, we characterized the genetic diversity of 34 P. melanocephala isolates from 4 Brazilian states using loci identified from an enriched simple sequence repeat (SSR) library. The aggressiveness of 3 isolates from major sugarcane cultivation areas was evaluated by inoculating an intermediately resistant and a susceptible cultivar. From the enriched library, 16 SSR-specific primers were developed, which produced scorable alleles. Of these, 4 loci were polymorphic and 12 were monomorphic for all isolates evaluated. The molecular characterization of the 34 isolates of P. melanocephala conducted using 16 SSR loci revealed the existence of low genetic variability among the isolates. The average estimated genetic distance was 0.12. Phenetic analysis based on Nei's genetic distance clustered the isolates into 2 major groups. Groups I and II included 18 and 14 isolates, respectively, and both groups contained isolates from all 4 geographic regions studied. Two isolates did not cluster with these groups. It was not possible to obtain clusters according to location or state of origin. Analysis of disease severity data revealed that the isolates did not show significant differences in aggressiveness between regions.

Phenotypic Heterogeneity of Genomically-Diverse Isolates of Streptococcus mutans

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Palmer, Sara R.; Miller, James H.; Abranches, Jacqueline; Zeng, Lin; Lefebure, Tristan; Richards, Vincent P.; Lemos, José A.; Stanhope, Michael J.; Burne, Robert A.

2013-01-01

High coverage, whole genome shotgun (WGS) sequencing of 57 geographically- and genetically-diverse isolates of Streptococcus mutans from individuals of known dental caries status was recently completed. Of the 57 sequenced strains, fifteen isolates, were selected based primarily on differences in gene content and phenotypic characteristics known to affect virulence and compared with the reference strain UA159. A high degree of variability in these properties was observed between strains, with a broad spectrum of sensitivities to low pH, oxidative stress (air and paraquat) and exposure to competence stimulating peptide (CSP). Significant differences in autolytic behavior and in biofilm development in glucose or sucrose were also observed. Natural genetic competence varied among isolates, and this was correlated to the presence or absence of competence genes, comCDE and comX, and to bacteriocins. In general strains that lacked the ability to become competent possessed fewer genes for bacteriocins and immunity proteins or contained polymorphic variants of these genes. WGS sequence analysis of the pan-genome revealed, for the first time, components of a Type VII secretion system in several S. mutans strains, as well as two putative ORFs that encode possible collagen binding proteins located upstream of the cnm gene, which is associated with host cell invasiveness. The virulence of these particular strains was assessed in a wax-worm model. This is the first study to combine a comprehensive analysis of key virulence-related phenotypes with extensive genomic analysis of a pathogen that evolved closely with humans. Our analysis highlights the phenotypic diversity of S. mutans isolates and indicates that the species has evolved a variety of adaptive strategies to persist in the human oral cavity and, when conditions are favorable, to initiate disease. PMID:23613838

Phenotypic heterogeneity of genomically-diverse isolates of Streptococcus mutans.

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Sara R Palmer

Full Text Available High coverage, whole genome shotgun (WGS sequencing of 57 geographically- and genetically-diverse isolates of Streptococcus mutans from individuals of known dental caries status was recently completed. Of the 57 sequenced strains, fifteen isolates, were selected based primarily on differences in gene content and phenotypic characteristics known to affect virulence and compared with the reference strain UA159. A high degree of variability in these properties was observed between strains, with a broad spectrum of sensitivities to low pH, oxidative stress (air and paraquat and exposure to competence stimulating peptide (CSP. Significant differences in autolytic behavior and in biofilm development in glucose or sucrose were also observed. Natural genetic competence varied among isolates, and this was correlated to the presence or absence of competence genes, comCDE and comX, and to bacteriocins. In general strains that lacked the ability to become competent possessed fewer genes for bacteriocins and immunity proteins or contained polymorphic variants of these genes. WGS sequence analysis of the pan-genome revealed, for the first time, components of a Type VII secretion system in several S. mutans strains, as well as two putative ORFs that encode possible collagen binding proteins located upstream of the cnm gene, which is associated with host cell invasiveness. The virulence of these particular strains was assessed in a wax-worm model. This is the first study to combine a comprehensive analysis of key virulence-related phenotypes with extensive genomic analysis of a pathogen that evolved closely with humans. Our analysis highlights the phenotypic diversity of S. mutans isolates and indicates that the species has evolved a variety of adaptive strategies to persist in the human oral cavity and, when conditions are favorable, to initiate disease.

Isolation of lactobacillus reuteri from Peyer's patches and their effects on sIgA production and gut microbiota diversity.

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Wang, Panpan; Li, Ya; Xiao, Hang; Shi, Yonghui; Le, Guo-Wei; Sun, Jin

2016-09-01

We previously reported that specific Lactobacillus reuteri colonized within mouse Peyer's patches (PP) effectively prevented high fat diet induced obesity and low-grade chronic inflammation. We further investigated the role of PP Lactobacillus reuteri on sIgA production in rats in this study. Lactobacilli were isolated from rat PP. All isolates were L. reuteri and belonged to three phenotypes according to amplified fragment length polymorphism analysis. Typical strains of two main clusters, PP1 and PP2, were used to treat control and vitamin A deficient (VAD) rats, respectively. The feeding of PP1 and PP2 affected sIgA and Lactobacillus diversity by strain-specific manner. Free sIgA was significantly increased by PP1 (p = 0.069) and PP2 (p Lactobacillus diversity in the control rats (p Lactobacillus diversity in both control and VAD rats. Fecal sIgA was correlated with PP Lactobacillus diversity (R(2) = 0.7958, p = 0.011). Modulation of sIgA production by PP L. reuteri of rat is dependent on vitamin A and change of Lactobacillus diversity in PP. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genetic diversity of Toxoplasma gondii isolates from Ethiopian feral cats.

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Dubey, J P; Choudhary, S; Tilahun, G; Tiao, N; Gebreyes, W A; Zou, X; Su, C

2013-09-01

Recent studies indicate greater genetic variability among isolates of Toxoplasma gondii worldwide than previously thought. However, there is no information on genetic diversity of T. gondii from any host in Ethiopia. In the present study, genotyping was performed on viable T. gondii isolates by bioassays in mice from tissues and feces of 27 cats from Ethiopia. Viable T. gondii was isolated from hearts of 26 cats, feces alone of 1 cat, and feces and tissues of 6 cats; in total there were 33 isolates. Genotyping was performed on DNA from cell-cultured derived T. gondii tachyzoites and by using 10 PCR-restriction fragment length polymorphism markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico). Four genotypes were recognized, including ToxoDB #1 (Type II clonal, nine isolates), ToxoDB #2 (Type III, five isolates), Toxo DB #3 (Type II variant, ten isolates), and ToxoDB #20 (nine isolates). Of interest is the isolation of different genotypes from tissues and feces of two cats, suggesting re-infection or mixed strain T. gondii infection. These findings are of epidemiological significance with respect to shedding of oocysts by cats. This is the first report of genotyping of T. gondii from any host in Ethiopia. Published by Elsevier B.V.

Porcine reproductive and respiratory syndrome virus: antigenic and molecular diversity of British isolates and implications for diagnosis.

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Frossard, Jean-Pierre; Fearnley, Catherine; Naidu, Brindha; Errington, Jane; Westcott, David G; Drew, Trevor W

2012-08-17

Porcine reproductive and respiratory syndrome (PRRS) is an endemic disease of pigs, caused by PRRS virus, a member of the Arteriviridae family. First seen in Britain in 1991, the disease continues to be a significant economic and welfare problem for pig producers. To date, only PRRSV genotype 1 has been found in Britain. At the genetic level, a considerable increase has been reported in the diversity of PRRS viruses isolated in Britain between 2003 and 2007, versus the early 1990 s. In this study, the diversity has been shown to extend to the antigenic level too, with potential consequences for diagnostic methods. Antigenic diversity was assessed using a panel of twelve monoclonal antibodies, only one of which reacted with all isolates tested. Nine diverse viruses were compared as potential antigens in immunoperoxidase monolayer assays, where each one produced quite different results for a common panel of sera. As a single virus is used in each diagnostic assay, results must therefore be interpreted cautiously. For a real-time RT-PCR assay, published oligonucleotide primer and probe sequences were evaluated against available genetic sequences of British and European viruses, and were re-designed where considerable mismatches were found. The multiplex assay incorporating these modified primers to detect genotype 1 and 2 PRRS viruses was then validated for use with diagnostic sera and tissues. As the increasing degree of diversity exhibited by British strains is mirrored in other countries, PRRSV will continue to provide an ongoing challenge to diagnosis at a global, as well as national level. Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved.

Isolation, diversity, and antimicrobial activity of rare actinobacteria from medicinal plants of tropical rain forests in Xishuangbanna, China.

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Qin, Sheng; Li, Jie; Chen, Hua-Hong; Zhao, Guo-Zhen; Zhu, Wen-Yong; Jiang, Cheng-Lin; Xu, Li-Hua; Li, Wen-Jun

2009-10-01

Endophytic actinobacteria are relatively unexplored as potential sources of novel species and novel natural products for medical and commercial exploitation. Xishuangbanna is recognized throughout the world for its diverse flora, especially the rain forest plants, many of which have indigenous pharmaceutical histories. However, little is known about the endophytic actinobacteria of this tropical area. In this work, we studied the diversity of actinobacteria isolated from medicinal plants collected from tropical rain forests in Xishuangbanna. By the use of different selective isolation media and methods, a total of 2,174 actinobacteria were isolated. Forty-six isolates were selected on the basis of their morphologies on different media and were further characterized by 16S rRNA gene sequencing. The results showed an unexpected level of diversity, with 32 different genera. To our knowledge, this is the first report describing the isolation of Saccharopolyspora, Dietzia, Blastococcus, Dactylosporangium, Promicromonospora, Oerskovia, Actinocorallia, and Jiangella species from endophytic environments. At least 19 isolates are considered novel taxa by our current research. In addition, all 46 isolates were tested for antimicrobial activity and were screened for the presence of genes encoding polyketide synthetases and nonribosomal peptide synthetases. The results confirm that the medicinal plants of Xishuangbanna represent an extremely rich reservoir for the isolation of a significant diversity of actinobacteria, including novel species, that are potential sources for the discovery of biologically active compounds.

Diversity and antibacterial activity of culturable actinobacteria isolated from five species of the South China Sea gorgonian corals.

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Zhang, Xiao-Yong; He, Fei; Wang, Guang-Hua; Bao, Jie; Xu, Xin-Ya; Qi, Shu-Hua

2013-06-01

This study describes the diversity and antibacterial activity of culturable actinobacteria isolated from five species of gorgonian corals (Echinogorgia aurantiaca, Melitodes squamata, Muricella flexuosa, Subergorgia suberosa, and Verrucella umbraculum) collected in shallow water of the South China Sea. A total of 123 actinobacterial isolates were recovered using ten different isolation media, and assigned to 11 genera, including Streptomyces and Micromonospora as the dominant genera, followed by Nocardia, Verrucosispora, Nocardiopsis, Rhodococcus, Pseudonocardia, Agrococcus, Saccharomonospora, Saccharopolyspora and Dietzia. Comparable analysis indicated that the numbers of actinobacterial genera and isolates from the five gorgonian coral species varied significantly. It was found that 72 isolates displayed antibacterial activity against at least one indicator bacterium, and the antibacterial strains isolated from different gorgonians had almost the same proportion (~50 %). These results provide direct evidence for the hypotheses that gorgonian coral species contain large and diverse communities of actinobacteria, and suggest that many gorgonian-associated actinobacteria could produce some antibacterial agents to protect their hosts against pathogens. To our knowledge, this is the first report about the diversity of culturable actinobacteria isolated from gorgonian corals.

Genetic Diversity Among Colletotrichum falcatum Isolates Causing Red Rot of Sugarcane in Subtropical Region of India

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Ratinderbir KAUR

2014-09-01

Full Text Available Silver Genetic diversity of Colletotrichum falcatum causing red rot of sugarcane was assessed based on morphological, pathological and molecular characteristics especially from sub-tropical Indian conditions. Sixteen isolates of this pathogen were collected based on the extensive survey on prominent varieties grown in the region along with some elite selections. Morphological observations (colony colour, mycelium pattern and sporulation grouped the isolates into two distinct types (C1: light type and C2: dark type. However, quantitative data on colony diameter showed five clusters for these isolates. Pathogenic characterization of these isolates on fourteen standard differentials formed six groups, ingroup 1: (CF-Pb-1 isolates Cf-157, Cf-249 and Cf-248 were the most virulent while group 6 (CF-Pb-6 isolates Cf-60 and Cf-247 were the least one. The genetic relatedness among the isolates using Random Amplified Polymorphic DNA (RAPD analysis revealed sufficient molecular polymorphism, which in turn confirmed the variation in virulence of different isolates. The data categorized different isolates into two major clusters and five independent lineages. Polymorphic information content (PIC ranged from 0.701 to 0.929. Isolate Cf-223 was found to be genetically most diverse among all the isolates. Present study inferred that morphological grouping of most of the isolates showed positive correlation with the pathogenic variability while molecular diversity did not showed such associations.

Consistent loss of genetic diversity in isolated cutthroat trout populations independent of habitat size and quality

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Kellie J. Carim; Lisa A. Eby; Craig A. Barfoot; Matthew C. Boyer

2016-01-01

Fragmentation and isolation of wildlife populations has reduced genetic diversity worldwide, leaving many populations vulnerable to inbreeding depression and local extinction. Nonetheless, isolation is protecting many native aquatic species from interactions with invasive species, often making reconnection an unrealistic conservation strategy. Isolation management is...

Diversity in UV sensitivity and recovery potential among bacterioneuston and bacterioplankton isolates.

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Santos, A L; Lopes, S; Baptista, I; Henriques, I; Gomes, N C M; Almeida, A; Correia, A; Cunha, A

2011-04-01

To assess the variability in UV-B (280-320 nm) sensitivity of selected bacterial isolates from the surface microlayer and underlying water of the Ria de Aveiro (Portugal) estuary and their ability to recover from previous UV-induced stress. Bacterial suspensions were exposed to UV-B radiation (3·3 W m⁻²). Effects on culturability and activity were assessed from colony counts and (3) H-leucine incorporation rates, respectively. Among the tested isolates, wide variability in UV-B-induced inhibition of culturability (37·4-99·3%) and activity (36·0-98·0%) was observed. Incubation of UV-B-irradiated suspensions under reactivating regimes (UV-A, 3·65 W m⁻²; photosynthetic active radiation, 40 W m⁻²; dark) also revealed diversity in the extent of recovery from UV-B stress. Trends of enhanced resistance of culturability (up to 15·0%) and enhanced recovery in activity (up to 52·0%) were observed in bacterioneuston isolates. Bacterioneuston isolates were less sensitive and recovered more rapidly from UV-B stress than bacterioplankton isolates, showing enhanced reduction in their metabolism during the irradiation period and decreased culturability during the recovery process compared to bacterioplankton. UV exposure can affect the diversity and activity of microbial communities by selecting UV-resistant strains and alter their metabolic activity towards protective strategies. © 2011 The Authors. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

Genetic diversity of Trichomonas vaginalis clinical isolates from Henan province in central China.

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Mao, Meng; Liu, Hui Li

2015-07-01

Trichomonas vaginalis is a flagellated protozoan parasite that infects the human urogenital tract, causing the most common non-viral, sexually transmitted disease worldwide. In this study, genetic variants of T. vaginalis were identified in Henan Province, China. Fragments of the small subunit of nuclear ribosomal RNA (18S rRNA) were amplified from 32 T. vaginalis isolates obtained from seven regions of Henan Province. Overall, 18 haplotypes were determined from the 18S rRNA sequences. Each sampled population and the total population displayed high haplotype diversity (Hd), accompanied by very low nucleotide diversity (Pi). In these molecular genetic variants, 91.58% genetic variation was derived from intra-regions. Phylogenetic analysis revealed no correlation between phylogeny and geographic distribution. Demographic analysis supported population expansion of T. vaginalis isolates from central China. Our findings showing moderate-to-high genetic variations in the 32 isolates of T. vaginalis provide useful knowledge for monitoring changes in parasite populations for the development of future control strategies.

Island Species Richness Increases with Habitat Diversity

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Hortal, J.; Triantis, K.A.; Meiri, S.; Thebault, E.M.C.; Sfenthourakis, S.

2009-01-01

Species richness is commonly thought to increase with habitat diversity. However, a recent theoretical model aiming to unify niche and island biogeography theories predicted a hump-shaped relationship between richness and habitat diversity. Given the contradiction between model results and previous

Genetic diversity of Escherichia coli isolates from surface water and groundwater in a rural environment.

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Gambero, Maria Laura; Blarasin, Monica; Bettera, Susana; Giuliano Albo, Jesica

2017-10-01

The genetic characteristics among Escherichia coli strains can be grouped by origin of isolation. Then, it is possible to use the genotypes as a tool to determine the source of water contamination. The aim of this study was to define water aptitude for human consumption in a rural basin and to assess the diversity of E. coli water populations. Thus, it was possible to identify the main sources of fecal contamination and to explore linkages with the hydrogeological environment and land uses. The bacteriological analysis showed that more than 50% of samples were unfit for human consumption. DNA fingerprinting analysis by BOX-PCR indicated low genotypic diversity of E. coli isolates taken from surface water and groundwater. The results suggested the presence of a dominant source of fecal contamination. The relationship between low genotypic diversity and land use would prove that water contamination comes from livestock. The genetic diversity of E. coli isolated from surface water was less than that identified in groundwater because of the different hydraulic features of both environments. Furthermore, each one of the two big strain groups identified in this basin is located in different sub-basins, showing that hydrological dynamics exerts selective pressure on bacteria DNA.

Antibiotic Susceptibility, Genetic Diversity, and the Presence of Toxin Producing Genes in Campylobacter Isolates from Poultry.

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Lee, Jeeyeon; Jeong, Jiyeon; Lee, Heeyoung; Ha, Jimyeong; Kim, Sejeong; Choi, Yukyung; Oh, Hyemin; Seo, Kunho; Yoon, Yohan; Lee, Soomin

2017-11-17

This study examined antibiotic susceptibility, genetic diversity, and characteristics of virulence genes in Campylobacter isolates from poultry. Chicken ( n = 152) and duck ( n = 154) samples were collected from 18 wet markets in Korea. Campylobacter spp. isolated from the carcasses were identified by PCR. The isolated colonies were analyzed for antibiotic susceptibility to chloramphenicol, amikacin, erythromycin, tetracycline, ciprofloxacin, nalidixic acid, and enrofloxacin. The isolates were also used to analyze genetic diversity using the DiversiLab TM system and were tested for the presence of cytolethal distending toxin ( cdt ) genes. Campylobacter spp. were isolated from 45 poultry samples out of 306 poultry samples (14.7%) and the average levels of Campylobacter contamination were 22.0 CFU/g and 366.1 CFU/g in chicken and duck samples, respectively. Moreover, more than 90% of the isolates showed resistance to nalidixic acid and ciprofloxacin. Genetic correlation analysis showed greater than 95% similarity between 84.4% of the isolates, and three cdt genes ( cdtA , cdtB , and cdtC ) were present in 71.1% of Campylobacter isolates. These results indicate that Campylobacter contamination should be decreased to prevent and treat Campylobacter foodborne illness.

Genetic diversity of human isolates of Salmonella enterica serovar Enteritidis in Malaysia.

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Bakeri, S A; Yasin, R M; Koh, Y T; Puthucheary, S D; Thong, K L

2003-01-01

The study was undertaken to determine clonal relationship and genetic diversity of the human strains of Salmonella enterica serovar Enteritidis isolated from 1995 to 2002 from different parts of Malaysia. Antimicrobial susceptibility test, plasmid profiling and pulsed-field gel electrophoresis were applied to analyse 65 human isolates of S. Enteritidis obtained over an eight year period from different parts of Malaysia. Four nonhuman isolates were included for comparison. A total of 14 distinct XbaI-pulsed-field profiles (PFPs) were observed, although a single PFP X1 was predominant and this particular clone was found to be endemic in Malaysia. The incidence of drug resistant S. Enteritidis remained relatively low with only 37% of the strains analysed being resistant to one or more antimicrobial agents. All except one resistant strain carried at least one plasmid ranging in size from 3.7 to 62 MDa giving nine plasmid profiles. The three isolates from raw milk and one from well-water had similar PFPs to that of the human isolates. Salmonella Enteritidis strains were more diverse than was previously thought. Fourteen subtypes were noted although one predominant clone persisted in Malaysia. The combination of pulsed-field gel electrophoresis, plasmid profiling and antibiograms provided additional discrimination to the highly clonal strains of S. Enteritidis. This is the first report to assess the genotypes of the predominant clinical S. Enteritidis in different parts of the country. As S. Enteritidis is highly endemic in Malaysia, the data generated would be useful for tracing the source during outbreaks of gastroenteritis in the study area.

Genetic diversity among brazilian isolates of beauveria bassiana: comparisons with non-brazilian isolates and other beauveria species

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Fernandes, E.K.K.; Moraes, A.M.L.; Pacheco, R.S.; Rangel, D.E.N.; Miller, M.P.; Bittencourt, V.R.E.P.; Roberts, D.W.

2009-01-01

Aims: The genetic diversity of Beauveria bassiana was investigated by comparing isolates of this species to each other (49 from different geographical regions of Brazil and 4 from USA) and to other Beauveria spp. Methods and Results: The isolates were examined by multilocus enzyme electrophoresis (MLEE), amplified fragment length polymorphism (AFLP), and rDNA sequencing. MLEE and AFLP revealed considerable genetic variability among B. bassiana isolates. Several isolates from South and Southeast Brazil had high similarity coefficients, providing evidence of at least one population with clonal structure. There were clear genomic differences between most Brazilian and USA B. bassiana isolates. A Mantel test using data generated by AFLP provided evidence that greater geographical distances were associated with higher genetic distances. AFLP and rDNA sequencing demonstrated notable genotypic variation between B. bassiana and other Beauveria spp. Conclusion: Geographical distance between populations apparently is an important factor influencing genotypic variability among B. bassiana populations in Brazil. Significance and Impact of the Study: This study characterized many B. bassiana isolates. The results indicate that certain Brazilian isolates are considerably different from others and possibly should be regarded as separate species from B. bassiana sensu latu. The information on genetic variation among the Brazilian isolates, therefore, will be important to comprehending the population structure of B. bassiana in Brazil. ?? 2009 The Society for Applied Microbiology.

Genetic and serological diversity of Flavobacterium psychrophilum isolates from salmonids in United Kingdom.

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Ngo, Thao P H; Bartie, Kerry L; Thompson, Kim D; Verner-Jeffreys, David W; Hoare, Rowena; Adams, Alexandra

2017-03-01

Flavobacterium psychrophilum is one of the most important bacterial pathogens affecting cultured rainbow trout (Oncorhynchus mykiss) and is increasingly causing problems in Atlantic salmon (Salmo salar L.) hatcheries. Little is known about the heterogeneity of F. psychrophilum isolates on UK salmonid farms. A total of 315 F. psychrophilum isolates, 293 of which were collected from 27 sites within the UK, were characterised using four genotyping methods and a serotyping scheme. A high strain diversity was identified among the isolates with 54 pulsotypes, ten (GTG) 5 -PCR types, two 16S rRNA allele lineages, seven plasmid profiles and three serotypes. Seven PFGE groups and 27 singletons were formed at a band similarity of 80%. PFGE group P (n=75) was found to be numerically predominant in eight sites within the UK. Two major PFGE clusters and 13 outliers were found at the band similarity of 40%. The predominant profileobserved within the F. psychrophilum isolates examined was PFGE cluster II - (GTG) 5 -PCR type r1-16S rRNA lineage II - serotype Th (70/156 isolates examined, 45%). Co-existence of genetically and serologically heterogeneous isolates within each farm was detected, confounding the ability to control RTFS outbreaks. The occurrence over time (up to 11 years) of F. psychrophilum pulsotypes in three representative sites (Scot I, Scot III and Scot V) within Scotland was examined, potentially providing important epidemiological data for farm management and the development of site-specific vaccines. Copyright © 2017 Elsevier B.V. All rights reserved.

Diversity and evolution of Lactobacillus casei group isolated from fermented dairy products in Tibet.

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Feng, Jing; Jiang, Yujun; Li, Mingyu; Zhao, Siyu; Zhang, Yanming; Li, Xuesong; Wang, Hui; Lin, Guangen; Wang, Hao; Li, Tiejing; Man, Chaoxin

2018-05-25

Bacteria in Lactobacillus casei group, including Lactobacillus casei (L. casei), Lactobacillus paracasei (L. paracasei), and Lactobacillus rhamnosus (L. rhamnosus) are important lactic acid bacteria in the production of fermented dairy products and are faced with the controversial nomenclatural status due to their close phylogenetic similarity. To probe the evolution and phylogeny of L. casei group, 100 isolates of lactic acid bacteria originated from naturally fermented dairy products in Tibet of China were subjected to multilocus sequence typing (MLST). The MLST scheme, based on analysis of the housekeeping genes fusA, ileS, lepA, leuS, pyrG, recA and recG, revealed that all the isolates belonged to a group containing the L. paracasei reference strains and were clearly different from the strains of L. casei and L. rhamnosus. Although nucleotide diversity (π) was low for the seven genes (ranging from 0.00341 for fusA to 0.01307 for recG), high genetic diversity represented by 83 sequence types (STs) with a discriminatory index of 0.98 was detected. A network-like structure based on split decomposition analysis, and the high values of the relative effect of recombination and mutation in the diversification of the lineages (r/m = 4.76) and the relative frequency of occurrence of recombination and mutation (ρ/θ = 2.62) indicated that intra-species recombination occurred frequently and homologous recombination played a key role in generating genotypic diversity amongst L. paracasei strains in Tibet. The discovery of 51 new STs and the results of STRUCTURE analysis suggested that the L. casei group in Tibet had an individual and particular population structure in comparison to European isolates. Overall, this research might be the first report about genetic diversity and population structure of Lactobacillus populations isolated from naturally fermented dairy products in Tibet based on MLST scheme.

Virulence and genetic diversity among isolates of Mycosphaerella fijiensis in two regions of Brazil.

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Silva, G F; Santos, V S; Sousa, N R; Hanada, R E; Gasparotto, L

2016-04-27

Black sigatoka, caused by the fungus Mycosphaerella fijiensis (anamorphic stage: Paracercospora fijiensis), was first detected in Brazil in early 1998 in the Benjamin Constant and Tabatinga municipalities in the State of Amazonas, near to where the borders of Brazil, Colombia, and Peru converge. Understanding how cultivars react to the pathogen, and characterizing the genetic variability of isolates from two distant and distinct banana-producing regions, are important for determining the virulence of M. fijiensis. In the present study, the genetic diversity of 22 M. fijiensis isolates was assessed using simple sequence repeats (SSR) markers, and their virulence was determined following inoculation on three different banana tree cultivars. All 22 isolates caused symptoms of the disease in the Maçã and Prata Comum cultivars 45 days after inoculation, and at least two virulence groups were identified for the Maçã and Prata Comum cultivars. For the D'Angola cultivars, two virulence groups were observed only after 60 days post-inoculation, and three of the isolates were not virulent. Using SSR markers, the isolates from two different regions of Brazil were placed into two genetic groups, both genetically distant from the Mf 138 isolate collected in Leticia, Colombia. There was no evidence of correlation between the virulence groups and the genetic diversity groups. These results demonstrate variability in virulence between isolates as measured by the severity of black sigatoka in the analyzed cultivars.

Antimicrobial Resistance Mechanisms and Genetic Diversity of Multidrug-Resistant Acinetobacter baumannii Isolated from a Teaching Hospital in Malaysia.

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Biglari, Shirin; Hanafiah, Alfizah; Mohd Puzi, Shaliawani; Ramli, Ramliza; Rahman, Mostafizur; Lopes, Bruno Silvester

2017-07-01

Multidrug-resistant (MDR) Acinetobacter baumannii has increasingly emerged as an important nosocomial pathogen. The aim of this study was to determine the resistance profiles and genetic diversity in A. baumannii clinical isolates in a tertiary medical center in Malaysia. The minimum inhibitory concentrations of carbapenems (imipenem and meropenem), cephalosporins (ceftazidime and cefepime), and ciprofloxacin were determined by E-test. PCR and sequencing were carried out for the detection of antibiotic resistance genes and mutations. Clonal relatedness among A. baumannii isolates was determined by REP-PCR. Sequence-based typing of OXA-51 and multilocus sequence typing were performed. One hundred twenty-five of 162 (77.2%) A. baumannii isolates had MDR phenotype. From the 162 A. baumannii isolates, 20 strain types were identified and majority of A. baumannii isolates (66%, n = 107) were classified as strain type 1 and were positive for ISAba1-bla OXA-23 and ISAba1-bla ADC and had mutations in both gyrA and parC genes at positions, 83 and 80, resulting in serine-to-leucine conversion. REP-PCR analysis showed 129 REP types that generated 31 clones with a 90% similarity cutoff value. OXA-66 variant of the bla OXA-51-like genes was predominantly detected among our A. baumannii clinical isolates belonging to ST195 (found in six clones: 1, 8, 9, 19, 27, and 30) and ST208 (found in clone 21). The study helps us in understanding the genetic diversity of A. baumannii isolates in our setting and confirms that international clone II is the most widely distributed clone in Universiti Kebangsaan Malaysia Medical Centre, Malaysia.

Characterization of Diazotrophs Containing Mo-Independent Nitrogenases, Isolated from Diverse Natural Environments▿

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Betancourt, Doris A.; Loveless, Telisa M.; Brown, James W.; Bishop, Paul E.

2008-01-01

Molybdenum-independent nitrogenases were first described in the nitrogen-fixing bacterium Azotobacter vinelandii and have since been described in other diazotrophic bacteria. Previously, we reported the isolation of seven diazotrophs with Mo-independent nitrogenases from aquatic environments. In the present study, we extend these results to include diazotrophs isolated from wood chip mulch, soil, “paraffin dirt,” and sediments from mangrove swamps. Mo-deficient, N-free media under both aerobic and anaerobic conditions were used for the isolations. A total of 26 isolates were genetically and physiologically characterized. Their phylogenetic placement was determined using 16S rRNA gene sequence analysis. Most of the isolates are members of the gamma subdivision of the class Proteobacteria and appear to be specifically related to fluorescent pseudomonads and azotobacteria. Two other isolates, AN1 and LPF4, are closely related to Enterobacter spp. and Paenibacillus spp., respectively. PCR and/or Southern hybridization were used to detect the presence of nitrogenase genes in the isolates. PCR amplification of vnfG and anfG was used to detect the genetic potential for the expression of the vanadium-containing nitrogenase and the iron-only nitrogenase in the isolates. This study demonstrates that diazotrophs with Mo-independent nitrogenases can be readily isolated from diverse natural environments. PMID:18378646

Diversity of genotypes in CTX-M-producing Klebsiella pneumoniae isolated in different hospitals in Brazil

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Thiago Pavoni Gomes Chagas

Full Text Available OBJECTIVE: The present study was undertaken to characterize CTX-M ESBL-producing Klebsiella pneumoniae collected from hospitals in different cities of Brazil. MATERIAL AND METHODS: Eighty-five K. pneumoniae strains isolated from hospitalized patients in six different hospitals of three cities of Brazil were analyzed. ESBL production was confirmed by the standard double-disk synergy test and the Etest®. The MIC50 and MIC90 for ESBL-producing isolates were determined by the Etest® method. The antimicrobial susceptibilities of bacterial isolates were determined using the agar diffusion method according to the CLSI. Screening for blaTEM, blaSHV, blaCTX-M genes and class 1 integron was performed by PCR amplification. To determine the genomic diversity of CTX-M-producers, isolates were analyzed by macrorestriction profile analysis following PFGE. RESULTS AND DISCUSSION: Seventy-one K. pneumoniae isolates were ESBL-producing. PCR and sequencing experiments detected 38 CTX-M-producing K. pneumoniae belonged to groups CTX-M 1, CTX-M 2, CTX-M 8 and CTX-M 9. The association of different types ESBL (CTX-M, SHV and TEM was frequent. All K. pneumoniae isolates carried class 1 integron. PFGE analysis revealed thirty-one clonal types among CTX-M-producing isolates. The data presented herein illustrate the diversity of genotypes of CTX-M producing K. pneumoniae among Brazilians hospitals.

Genetic Diversity and Differentiation of Colletotrichum spp. Isolates Associated with Leguminosae Using Multigene Loci, RAPD and ISSR

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Farshid Mahmodi

2014-03-01

Full Text Available Genetic diversity and differentiation of 50 Colletotrichum spp. isolates from legume crops studied through multigene loci, RAPD and ISSR analysis. DNA sequence comparisons by six genes (ITS, ACT, Tub2, CHS-1, GAPDH, and HIS3 verified species identity of C. truncatum, C. dematium and C. gloeosporiodes and identity C. capsici as a synonym of C. truncatum. Based on the matrix distance analysis of multigene sequences, the Colletotrichum species showed diverse degrees of intera and interspecific divergence (0.0 to 1.4% and (15.5–19.9, respectively. A multilocus molecular phylogenetic analysis clustered Colletotrichum spp. isolates into 3 well-defined clades, representing three distinct species; C. truncatum, C. dematium and C. gloeosporioides. The ISSR and RAPD and cluster analysis exhibited a high degree of variability among different isolates and permitted the grouping of isolates of Colletotrichum spp. into three distinct clusters. Distinct populations of Colletotrichum spp. isolates were genetically in accordance with host specificity and inconsistent with geographical origins. The large population of C. truncatum showed greater amounts of genetic diversity than smaller populations of C. dematium and C. gloeosporioides species. Results of ISSR and RAPD markers were congruent, but the effective maker ratio and the number of private alleles were greater in ISSR markers.

Selection of cellulolytic fungi isolated from diverse substrates

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Mônica Caramez Triches Damaso

2012-08-01

Full Text Available The aim of the present work was to select filamentous fungi isolated from diverse substrates to obtain the strains with potential to produce the hydrolytic enzymes. From a total of 215 strains, seven strains from the soils, six from the plants and one from sugarcane bagasse were selected and identified as belonging to the Trichoderma, Penicillium and Aspergillus genera. The best hydrolytic activities obtained by semi-solid fermentation using these strains were approximately: 35; 1; 160; 170 and 120 U/gdm (CMCase, FPase, β-glucosidase, xylanase and polygalacturonase, respectively, demonstrating their potential to synthesize the enzymes compared with the results reported in the literature.

Isolation of diverse members of the Aquificales from geothermal springs in Tengchong, China

OpenAIRE

Hedlund, Brian P.; Reysenbach, Anna-Louise; Huang, Liuquin; Ong, John C.; Liu, Zizhang; Dodsworth, Jeremy A.; Ahmed, Reham; Williams, Amanda J.; Briggs, Brandon R.; Liu, Yitai; Hou, Weiguo; Dong, Hailiang

2015-01-01

The order Aquificales (phylum Aquificae) consists of thermophilic and hyperthermophilic bacteria that are prominent in many geothermal systems, including those in Tengchong, Yunnan Province, China. However, Aquificales have not previously been isolated from Tengchong. We isolated five strains of Aquificales from diverse springs (temperature 45.2–83.3°C and pH 2.6–9.1) in the Rehai Geothermal Field from sites in which Aquificales were abundant. Phylogenetic analysis showed that four of the str...

Increased extinction potential of insular fish populations with reduced life history variation and low genetic diversity.

Science.gov (United States)

Hellmair, Michael; Kinziger, Andrew P

2014-01-01

Theoretical work has shown that reduced phenotypic heterogeneity leads to population instability and can increase extinction potential, yet few examples exist of natural populations that illustrate how varying levels expressed diversity may influence population persistence, particularly during periods of stochastic environmental fluctuation. In this study, we assess levels of expressed variation and genetic diversity among demographically independent populations of tidewater goby (Eucyclogobius newberryi), show that reductions in both factors typically coincide, and describe how low levels of diversity contribute to the extinction risk of these isolated populations. We illustrate that, for this annual species, continuous reproduction is a safeguard against reproductive failure by any one population segment, as natural, stochastically driven salinity increases frequently result in high mortality among juvenile individuals. Several study populations deviated from the natural pattern of year-round reproduction typical for the species, rendering those with severely truncated reproductive periods vulnerable to extinction in the event of environmental fluctuation. In contrast, demographically diverse populations are more likely to persist through such periods through the continuous presence of adults with broader physiological tolerance to abrupt salinity changes. Notably, we found a significant correlation between genetic diversity and demographic variation in the study populations, which could be the result of population stressors that restrict both of these diversity measures simultaneously, or suggestive of a causative relationship between these population characteristics. These findings demonstrate the importance of biocomplexity at the population level, and assert that the maintenance of diversity contributes to population resilience and conservation of this endangered species.

Increased extinction potential of insular fish populations with reduced life history variation and low genetic diversity.

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Michael Hellmair

Full Text Available Theoretical work has shown that reduced phenotypic heterogeneity leads to population instability and can increase extinction potential, yet few examples exist of natural populations that illustrate how varying levels expressed diversity may influence population persistence, particularly during periods of stochastic environmental fluctuation. In this study, we assess levels of expressed variation and genetic diversity among demographically independent populations of tidewater goby (Eucyclogobius newberryi, show that reductions in both factors typically coincide, and describe how low levels of diversity contribute to the extinction risk of these isolated populations. We illustrate that, for this annual species, continuous reproduction is a safeguard against reproductive failure by any one population segment, as natural, stochastically driven salinity increases frequently result in high mortality among juvenile individuals. Several study populations deviated from the natural pattern of year-round reproduction typical for the species, rendering those with severely truncated reproductive periods vulnerable to extinction in the event of environmental fluctuation. In contrast, demographically diverse populations are more likely to persist through such periods through the continuous presence of adults with broader physiological tolerance to abrupt salinity changes. Notably, we found a significant correlation between genetic diversity and demographic variation in the study populations, which could be the result of population stressors that restrict both of these diversity measures simultaneously, or suggestive of a causative relationship between these population characteristics. These findings demonstrate the importance of biocomplexity at the population level, and assert that the maintenance of diversity contributes to population resilience and conservation of this endangered species.

Genetic diversity of pestivirus isolates in cattle from Western Austria.

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Hornberg, Andrea; Fernández, Sandra Revilla; Vogl, Claus; Vilcek, Stefan; Matt, Monika; Fink, Maria; Köfer, Josef; Schöpf, Karl

2009-03-30

The genetic diversity of bovine viral diarrhoea virus (BVDV) isolates in infected cattle from Tyrol and Vorarlberg (Austria) was investigated. Blood samples were collected within the compulsory Austrian BVDV control programme during 2005 and 2006. The 5'-untranslated region (5'-UTR) and partially the N-terminal autoprotease (N(pro)) were amplified by one-step reverse transcriptase-polymerase chain reaction (RT-PCR) and the PCR products were subsequently sequenced. Phylogenetic analysis based on 5'-UTR and N(pro) sequences demonstrated that almost all isolates (307/310) were of the BVDV-1 genotype. They were clustered into eight different subtypes, here listed by their frequency of occurrence: BVDV-1h (143), BVDV-1f (79), BVDV-1b (41), BVDV-1d (28), BVDV-1e (6), BVDV-1a (4), BVDV-1g (3) and BVDV1-k (3). Two pestivirus isolates were typed as BVDV-2 and one isolate as BDV closely related to Gifhorn strain (BDV-3). Correlation among isolates could only be observed at the farm level, i.e., within a herd. However, no correlation between the genetic and geographical distances could be observed above the farm level. Because of the wide distribution of certain BVDV-1 subtypes and the low prevalence of herd-specific strains, a determination of tracing routes of infection was not possible. Furthermore, recombination events were not detected.

Impact of enumeration method on diversity of Escherichia coli genotypes isolated from surface water.

Science.gov (United States)

Martin, E C; Gentry, T J

2016-11-01

There are numerous regulatory-approved Escherichia coli enumeration methods, but it is not known whether differences in media composition and incubation conditions impact the diversity of E. coli populations detected by these methods. A study was conducted to determine if three standard water quality assessments, Colilert ® , USEPA Method 1603, (modified mTEC) and USEPA Method 1604 (MI), detect different populations of E. coli. Samples were collected from six watersheds and analysed using the three enumeration approaches followed by E. coli isolation and genotyping. Results indicated that the three methods generally produced similar enumeration data across the sites, although there were some differences on a site-by-site basis. The Colilert ® method consistently generated the least diverse collection of E. coli genotypes as compared to modified mTEC and MI, with those two methods being roughly equal to each other. Although the three media assessed in this study were designed to enumerate E. coli, the differences in the media composition, incubation temperature, and growth platform appear to have a strong selective influence on the populations of E. coli isolated. This study suggests that standardized methods of enumeration and isolation may be warranted if researchers intend to obtain individual E. coli isolates for further characterization. This study characterized the impact of three USEPA-approved Escherichia coli enumeration methods on observed E. coli population diversity in surface water samples. Results indicated that these methods produced similar E. coli enumeration data but were more variable in the diversity of E. coli genotypes observed. Although the three methods enumerate the same species, differences in media composition, growth platform, and incubation temperature likely contribute to the selection of different cultivable populations of E. coli, and thus caution should be used when implementing these methods interchangeably for

Diversity and Seasonal Variation of Endophytic Fungi Isolated from Three Conifers in Mt. Taehwa, Korea

OpenAIRE

Kim, Chang-Kyun; Eo, Ju-Kyeong; Eom, Ahn-Heum

2013-01-01

The needled leaves of three conifer species were collected in Mt. Taehwa during different seasons of the year. Total 59 isolates and 19 species of endophytic fungi were isolated from the leaves and identified using morphological and molecular characteristics. As a result, Shannon index was different in its host plant; Larix kaempferi had a highest value of species diversity. According to the sampling season, 9 species of 19 species were isolated during fall season. The results suggest that th...

Isolation and characterization of numerous novel phages targeting diverse strains of the ubiquitous and opportunistic pathogen Achromobacter xylosoxidans.

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Johannes Wittmann

Full Text Available The clinical relevance of nosocomially acquired infections caused by multi-resistant Achromobacter strains is rapidly increasing. Here, a diverse set of 61 Achromobacter xylosoxidans strains was characterized by MultiLocus Sequence Typing and Phenotype MicroArray technology. The strains were further analyzed in regard to their susceptibility to 35 antibiotics and to 34 different and newly isolated bacteriophages from the environment. A large proportion of strains were resistant against numerous antibiotics such as cephalosporines, aminoglycosides and quinolones, whereas piperacillin-tazobactam, ticarcillin, mezlocillin and imipenem were still inhibitory. We also present the first expanded study on bacteriophages of the genus Achromobacter that has been so far a blank slate with respect to phage research. The phages were isolated mainly from several waste water treatment plants in Germany. Morphological analysis of all of these phages by electron microscopy revealed a broad diversity with different members of the order Caudovirales, including the families Siphoviridae, Myoviridae, and Podoviridae. A broad spectrum of different host ranges could be determined for several phages that lysed up to 24 different and in part highly antibiotic resistant strains. Molecular characterisation by DNA restriction analysis revealed that all phages contain linear double-stranded DNA. Their restriction patterns display distinct differences underlining their broad diversity.

Genetic diversity and occurrence of the F129L substitutions among isolates of Alternaria solani in south-eastern Sweden.

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Odilbekov, Firuz; Edin, Eva; Garkava-Gustavsson, Larisa; Hovmalm, Helena Persson; Liljeroth, Erland

2016-01-01

Early blight, caused by the fungus Alternaria solani, occurs on potato mainly in the south-eastern part of Sweden, but also in other parts of the country. The aim of this study was to investigate the genetic diversity of A. solani populations from different potato growing regions in south-eastern Sweden using AFLP marker analysis. In addition, the cultured isolates were examined for substitutions in the gene encoding cytochrome b , associated with loss of sensitivity against QoI fungicides. Nei's gene diversity index for the Swedish populations of A. solani revealed a gene diversity of up to 0.20. Also genetic differentiation was observed among populations of A. solani from different locations in south-eastern Sweden. The mitochondrial genotype of the isolates of A. solani was determined and both known genotypes, GI (genotype 1) and GII (genotype 2), were found among the isolates. The occurrence of the F129L substitution associated with a loss of sensitivity to strobilurins was confirmed among the GII isolates. In vitro conidial germination tests verified that isolates containing the F129L substitution had reduced sensitivity to azoxystrobin and, at a lower extent, to pyraclostrobin. Genetic diversity was relatively high among isolates of A. solani in south-eastern part of Sweden. F129L substitutions, leading to reduced sensitivity to strobilurins, have been established in field populations, which may have implications for the future efficacy of QoI fungicides.

Isolation of novel microsatellites using FIASCO by dual probe enrichment from Jatropha curcas L. and study on genetic equilibrium and diversity of Indian population revealed by isolated microsatellites

KAUST Repository

Pamidimarri, D. V N N Sudheer

2010-03-11

Jatropha curcas L. belongs to family Euphorbiaceae, native to South America attained significant importance for its seed oil which can be converted to biodiesel, a renewable energy source alternative to conventional petrodiesel. Very few attempts were made to isolate novel microsatellite markers and assessment of the extent of genetic equilibrium and diversity that exists in J. curcas. Therefore, the present investigation was undertaken to isolate the novel microsatellites and access genetic equilibrium, diversity that exists among 44 diverse germplasm collected from distinct geographical areas in India using isolated microsatellites. The overall efficiency of the enrichment of microsatellite by dual probe in the present study found to be 54% and among the sequences obtained the percentage of sequences having suitable flanking regions for the primer designing was found to be 89.58%. The mean co-efficient of genetic similarity (CGS) was found to be 0.97. The overall diversity obtained by microsatellites was found to be low in comparison with the diversity reported by multilocus markers systems observed in earlier studies; however, the good allele polymorphism was observed. The overall dendrogram of microsatellite analysis resulted in random clustering of germplasm and not in accordance to geographical area of collection. The present study, diversity analysis using microsatellite markers concludes the low genetic diversity and genetic disequlibrium of J. curcas in India and will provide pavement for further intra-population studies on narrow geographical areas to understand the population genetic structure, phylogeography and molecular ecological studies. The germplasm characterized, and the microsatellite markers isolated and characterized in the present study can be employed efficiently in breeding programs for genetic improvement of the species through marker assisted selection and QTL analysis, for further genetic resource management and help in making the J

Assessment of Genetic Diversity among Pleurotus spp. Isolates from Jordan

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Hanan Aref Hasan

2018-04-01

Full Text Available Pleurotus is considered an important genus that belongs to the family Pleurotaceae and includes the edible King Oyster mushroom (Pleurotus eryngii. In the present study, 19 Pleurotus isolates were collected from two locations in the north of Jordan (Tell ar-Rumman and Um-Qais. The morphological characteristics among collected isolates revealed that there was a morphological similarity among the collected isolates. Nucleotide sequence analysis of the internal transcribed spacer (ITS1–5.8S rDNA–ITS4 region and 28S nuclear large subunit (nLSU in the ribosomal DNA gene of the isolated stains showed that all of them share over 98% sequence similarity with P. eryngii. Genetic diversity among the collected strains was assessed using inter simple sequence repeat (ISSR analysis using 18 different primer pairs. Using this approach, 141 out of 196 bands obtained were considered polymorphic and the highest percentage of polymorphism was observed using primer UBC827 (92.3% with an overall Polymorphism Information Content (PIC value of 70.56%. Cluster analysis showed that the Jordanian Pleurotus isolates fall into two main clades with a coefficient of similarity values ranging from 0.59 to 0.74 with a clear clustering based on collection sites. The results of the present study reveal that molecular techniques of ISSR and rDNA sequencing can greatly aid in classification and identification of Pleurotus spp. in Jordan.

The biological features and genetic diversity of novel fish rhabdovirus isolates in China.

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Fu, Xiaozhe; Lin, Qiang; Liang, Hongru; Liu, Lihui; Huang, Zhibin; Li, Ningqiu; Su, Jianguo

2017-09-01

The Rhabdoviridae is a diverse family of negative-sense single-stranded RNA viruses which infects mammals, birds, reptiles, fish, insects and plants. Herein, we reported the isolation and characterization of 6 novel viruses from diseased fish collected from China including SCRV-QY, SCRV-SS, SCRV-GM, CmRV-FS, MsRV-SS, OmbRV-JM. The typical clinical symptom of diseased fish was hemorrhaging. Efficient propagation of these isolates in a Chinese perch brain cell line was determined by means of observation of cytopathic effect, RT-PCR and electron microscopy. Sequence alignment and phylogenetic analysis of the complete G protein sequences revealed that these isolates were clustered into one monophyletic lineage belonging to the species Siniperca chuatsi rhabdovirus.

Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints.

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Stefan Niemann

2009-10-01

Full Text Available Mycobacterium tuberculosis complex (MTBC, the causative agent of tuberculosis (TB, is characterized by low sequence diversity making this bacterium one of the classical examples of a genetically monomorphic pathogen. Because of this limited DNA sequence variation, routine genotyping of clinical MTBC isolates for epidemiological purposes relies on highly discriminatory DNA fingerprinting methods based on mobile and repetitive genetic elements. According to the standard view, isolates exhibiting the same fingerprinting pattern are considered direct progeny of the same bacterial clone, and most likely reflect ongoing transmission or disease relapse within individual patients.Here we further investigated this assumption and used massively parallel whole-genome sequencing to compare one drug-susceptible (K-1 and one multidrug resistant (MDR isolate (K-2 of a rapidly spreading M. tuberculosis Beijing genotype clone from a high incidence region (Karakalpakstan, Uzbekistan. Both isolates shared the same IS6110 RFLP pattern and the same allele at 23 out of 24 MIRU-VNTR loci. We generated 23.9 million (K-1 and 33.0 million (K-2 paired 50 bp purity filtered reads corresponding to a mean coverage of 483.5 fold and 656.1 fold respectively. Compared with the laboratory strain H37Rv both Beijing isolates shared 1,209 SNPs. The two Beijing isolates differed by 130 SNPs and one large deletion. The susceptible isolate had 55 specific SNPs, while the MDR variant had 75 specific SNPs, including the five known resistance-conferring mutations.Our results suggest that M. tuberculosis isolates exhibiting identical DNA fingerprinting patterns can harbour substantial genomic diversity. Because this heterogeneity is not captured by traditional genotyping of MTBC, some aspects of the transmission dynamics of tuberculosis could be missed or misinterpreted. Furthermore, a valid differentiation between disease relapse and exogenous reinfection might be impossible using

Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints.

Science.gov (United States)

Niemann, Stefan; Köser, Claudio U; Gagneux, Sebastien; Plinke, Claudia; Homolka, Susanne; Bignell, Helen; Carter, Richard J; Cheetham, R Keira; Cox, Anthony; Gormley, Niall A; Kokko-Gonzales, Paula; Murray, Lisa J; Rigatti, Roberto; Smith, Vincent P; Arends, Felix P M; Cox, Helen S; Smith, Geoff; Archer, John A C

2009-10-12

Mycobacterium tuberculosis complex (MTBC), the causative agent of tuberculosis (TB), is characterized by low sequence diversity making this bacterium one of the classical examples of a genetically monomorphic pathogen. Because of this limited DNA sequence variation, routine genotyping of clinical MTBC isolates for epidemiological purposes relies on highly discriminatory DNA fingerprinting methods based on mobile and repetitive genetic elements. According to the standard view, isolates exhibiting the same fingerprinting pattern are considered direct progeny of the same bacterial clone, and most likely reflect ongoing transmission or disease relapse within individual patients. Here we further investigated this assumption and used massively parallel whole-genome sequencing to compare one drug-susceptible (K-1) and one multidrug resistant (MDR) isolate (K-2) of a rapidly spreading M. tuberculosis Beijing genotype clone from a high incidence region (Karakalpakstan, Uzbekistan). Both isolates shared the same IS6110 RFLP pattern and the same allele at 23 out of 24 MIRU-VNTR loci. We generated 23.9 million (K-1) and 33.0 million (K-2) paired 50 bp purity filtered reads corresponding to a mean coverage of 483.5 fold and 656.1 fold respectively. Compared with the laboratory strain H37Rv both Beijing isolates shared 1,209 SNPs. The two Beijing isolates differed by 130 SNPs and one large deletion. The susceptible isolate had 55 specific SNPs, while the MDR variant had 75 specific SNPs, including the five known resistance-conferring mutations. Our results suggest that M. tuberculosis isolates exhibiting identical DNA fingerprinting patterns can harbour substantial genomic diversity. Because this heterogeneity is not captured by traditional genotyping of MTBC, some aspects of the transmission dynamics of tuberculosis could be missed or misinterpreted. Furthermore, a valid differentiation between disease relapse and exogenous reinfection might be impossible using standard

Evidence for high genetic diversity of NAD1 and COX1 mitochondrial haplotypes among triclabendazole resistant and susceptible populations and field isolates of Fasciola hepatica (liver fluke) in Australia.

Science.gov (United States)

Elliott, T; Muller, A; Brockwell, Y; Murphy, N; Grillo, V; Toet, H M; Anderson, G; Sangster, N; Spithill, T W

2014-02-24

In recent years, the global incidence of Fasciola hepatica (liver fluke) infections exhibiting resistance to triclabendazole (TCBZ) has increased, resulting in increased economic losses for livestock producers and threatening future control. The development of TCBZ resistance and the worldwide discovery of F. hepatica population diversity has emphasized the need to further understand the genetic structure of drug susceptible and resistant Fasciola populations within Australia. In this study, the genetic diversity of liver flukes was estimated by sequencing mitochondrial DNA (mtDNA) encoding the NAD1 (530 bp) and COX1 (420 bp) genes of 208 liver flukes (F. hepatica) collected from three populations: field isolates obtained from abattoirs from New South Wales (NSW) and Victoria (Vic); three TCBZ-resistant fluke populations from NSW and Victoria; and the well-established TCBZ-susceptible Sunny Corner laboratory isolate. Overall nucleotide diversity for all flukes analysed of 0.00516 and 0.00336 was estimated for the NAD1 and COX1 genes respectively. Eighteen distinct haplotypes were established for the NAD1 gene and six haplotypes for the COX1 gene, resulting in haplotype diversity levels of 0.832 and 0.482, respectively. One field isolate showed a similar low level of haplotype diversity as seen in the Sunny Corner laboratory isolate. Analysis of TCBZ-resistant infrapopulations from 3 individual cattle grazing one property revealed considerable sequence parasite diversity between cattle. Analysis of parasite TCBZ-resistant infrapopulations from sheep and cattle revealed haplotypes unique to each host, but no significant difference between parasite populations. Fst analysis of fluke populations revealed little differentiation between the resistant and field populations. This study has revealed a high level of diversity in field and drug resistant flukes in South-Eastern Australia. Copyright © 2013 Elsevier B.V. All rights reserved.

Genotypic and Phenotypic Diversity of Cryptococcus gattii VGII Clinical Isolates and Its Impact on Virulence

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Vanessa A. Barcellos

2018-02-01

Full Text Available The Cryptococcus gattii species complex harbors the main etiological agents of cryptococcosis in immunocompetent patients. C. gattii molecular type VGII predominates in the north and northeastern regions of Brazil, leading to high morbidity and mortality rates. C. gattii VGII isolates have a strong clinical relevance and phenotypic variations. These phenotypic variations among C. gattii species complex isolates suggest that some strains are more virulent than others, but little information is available related to the pathogenic properties of those strains. In this study, we analyzed some virulence determinants of C. gattii VGII strains (CG01, CG02, and CG03 isolated from patients in the state of Piauí, Brazil. The C. gattii R265 VGIIa strain, which was isolated from the Vancouver outbreak, differed from C. gattii CG01, CG02 and CG03 isolates (also classified as VGII when analyzed the capsular dimensions, melanin production, urease activity, as well as the glucuronoxylomannan (GXM secretion. Those differences directly reflected in their virulence potential. In addition, CG02 displayed higher virulence compared to R265 (VGIIa strain in a cryptococcal murine model of infection. Lastly, we examined the genotypic diversity of these strains through Multilocus Sequence Type (MLST and one new subtype was described for the CG02 isolate. This study confirms the presence and the phenotypic and genotypic diversity of highly virulent strains in the Northeast region of Brazil.

Genetic diversity and antimicrobial resistance of Campylobacter and Salmonella strains isolated from decoys and raptors.

Science.gov (United States)

Jurado-Tarifa, E; Torralbo, A; Borge, C; Cerdà-Cuéllar, M; Ayats, T; Carbonero, A; García-Bocanegra, I

2016-10-01

Infections caused by thermotolerant Campylobacter spp. and Salmonella spp. are the leading causes of human gastroenteritis worldwide. Wild birds can act as reservoirs of both pathogens. A survey was carried out to determine the prevalence, genetic diversity and antimicrobial resistance of thermotolerant Campylobacter and Salmonella in waterfowl used as decoys and wild raptors in Andalusia (Southern Spain). The overall prevalence detected for Campylobacter was 5.9% (18/306; CI95%: 3.25-8.52) in decoys and 2.3% (9/387; CI95%: 0.82-3.83) in wild raptors. Isolates were identified as C. jejuni, C. coli and C. lari in both bird groups. Salmonella was isolated in 3.3% (10/306; CI95%: 2.3-4.3) and 4.6% (18/394; CI95%: 3.5-5.6) of the decoys and raptors, respectively. Salmonella Enteritidis and Typhimurium were the most frequently identified serovars, although Salmonella serovars Anatum, Bredeney, London and Mikawasima were also isolated. Pulsed-field gel electrophoresis analysis of isolates showed higher genetic diversity within Campylobacter species compared to Salmonella serovars. Campylobacter isolates showed resistance to gentamicin, ciprofloxacin and tetracycline, while resistance to erythromycin and tetracycline was found in Salmonella isolates. The results indicate that both decoys and raptors can act as natural carriers of Campylobacter and Salmonella in Spain, which may have important implications for public and animal health. Copyright © 2016 Elsevier Ltd. All rights reserved.

Assessment of intra-species diversity among strains of Acinetobacter baumannii isolated from sites contaminated with petroleum hydrocarbons

International Nuclear Information System (INIS)

Manab Sarma, P.; Bhattacharya, D.; Krishnan, S.; Lal, B.

2004-01-01

Intra-species diversity among Acinetobacter baumannii strains isolated from crude oil-contaminated soils from different geographic regions in India was assessed, including their capability to degrade different fractions of total petroleum hydrocarbons. A total of 96 strains were isolated from five different sites. Of the 96 isolates, 25 strains were identified as Acinetobacter baumannii; all of these strains were biochemically profiled and grouped into eight phenovars on the basis of multivariate analysis of their substrate utilization profiles. All strains were able to degrade the total petroleum hydrocarbon fractions of crude oil. Intraspecies relatedness among the 25 strains was determined using tRNA intergenic spacer length polymorphism. Specific variants among the strains with different degradation capacities for different fractions of crude oil were detected. Environmental influences that cause intra-species diversity, such as functional resilience, within the selected strains of A. baumannii were also noted. It is suggested that such diversities may make it possible to select contaminant-specific strains for efficient biotechnological strategies in environmental remediation. 19 refs., 4 tabs., 3 figs

Assessment of intra-species diversity among strains of Acinetobacter baumannii isolated from sites contaminated with petroleum hydrocarbons

Energy Technology Data Exchange (ETDEWEB)

Manab Sarma, P.; Bhattacharya, D.; Krishnan, S. [TERI School of Advanced Studies, Center of Bioresources and Biotechnology, New Delhi (India); Lal, B. [TERI School of Advanced Studies, Microbial Biotechnology Division, New Delhi (India)

2004-06-01

Intra-species diversity among Acinetobacter baumannii strains isolated from crude oil-contaminated soils from different geographic regions in India was assessed, including their capability to degrade different fractions of total petroleum hydrocarbons. A total of 96 strains were isolated from five different sites. Of the 96 isolates, 25 strains were identified as Acinetobacter baumannii; all of these strains were biochemically profiled and grouped into eight phenovars on the basis of multivariate analysis of their substrate utilization profiles. All strains were able to degrade the total petroleum hydrocarbon fractions of crude oil. Intraspecies relatedness among the 25 strains was determined using tRNA intergenic spacer length polymorphism. Specific variants among the strains with different degradation capacities for different fractions of crude oil were detected. Environmental influences that cause intra-species diversity, such as functional resilience, within the selected strains of A. baumannii were also noted. It is suggested that such diversities may make it possible to select contaminant-specific strains for efficient biotechnological strategies in environmental remediation. 19 refs., 4 tabs., 3 figs.

Diversity and seasonal variation of endophytic fungi isolated from three conifers in mt. Taehwa, Korea.

Science.gov (United States)

Kim, Chang-Kyun; Eo, Ju-Kyeong; Eom, Ahn-Heum

2013-06-01

The needled leaves of three conifer species were collected in Mt. Taehwa during different seasons of the year. Total 59 isolates and 19 species of endophytic fungi were isolated from the leaves and identified using morphological and molecular characteristics. As a result, Shannon index was different in its host plant; Larix kaempferi had a highest value of species diversity. According to the sampling season, 9 species of 19 species were isolated during fall season. The results suggest that the existing of host plant and sampling season are major factors of distribution of endophytic fungi.

Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures.

Science.gov (United States)

Wilkins, Laetitia G E; Rogivue, Aude; Schütz, Frédéric; Fumagalli, Luca; Wedekind, Claus

2015-11-27

The taxonomic composition of egg-associated microbial communities can play a crucial role in the development of fish embryos. In response, hosts increasingly influence the composition of their associated microbial communities during embryogenesis, as concluded from recent field studies and laboratory experiments. However, little is known about the taxonomic composition and the diversity of egg-associated microbial communities within ecosystems; e.g., river networks. We sampled late embryonic stages of naturally spawned brown trout at nine locations within two different river networks and applied 16S rRNA pyrosequencing to describe their bacterial communities. We found no evidence for a significant isolation-by-distance effect on the composition of bacterial communities, and no association between neutral genetic divergence of fish host (based on 11 microsatellites) and phylogenetic distances of the composition of their associated bacterial communities. We characterized core bacterial communities on brown trout eggs and compared them to corresponding water samples with regard to bacterial composition and its presumptive function. Bacterial diversity was positively correlated with water temperature at the spawning locations. We discuss this finding in the context of the increased water temperatures that have been recorded during the last 25 years in the study area.

Genetic diversity of clinical and environmental strains of Salmonella enterica serotype Weltevreden isolated in Malaysia.

Science.gov (United States)

Thong, K L; Goh, Y L; Radu, S; Noorzaleha, S; Yasin, R; Koh, Y T; Lim, V K E; Rusul, G; Puthucheary, S D

2002-07-01

The incidence of food-borne salmonellosis due to Salmonella enterica serotype Weltevreden is reported to be on the increase in Malaysia. The pulsed-field gel electrophoresis (PFGE) subtyping method was used to assess the extent of genetic diversity and clonality of Salmonella serotype Weltevreden strains from humans and the environment. PFGE of XbaI-digested chromosomal DNA from 95 strains of Salmonella serotype Weltevreden gave 39 distinct profiles with a wide range of Dice coefficients (0.27 to 1.00), indicating that PFGE is very discriminative and that multiple clones of Salmonella serotype Weltevreden exist among clinical and environmental isolates. Strains of one dominant pulsotype (pulsotype X1/X2) appeared to be endemic in this region, as they were consistently recovered from humans with salmonellosis between 1996 and 2001 and from raw vegetables. In addition, the sharing of similar PFGE profiles among isolates from humans, vegetables, and beef provides indirect evidence of the possible transmission of salmonellosis from contaminated raw vegetables and meat to humans. Furthermore, the recurrence of PFGE profile X21 among isolates found in samples of vegetables from one wet market indicated the persistence of this clone. The environment in the wet markets may represent a major source of cross-contamination of vegetables with Salmonella serotype Weltevreden. Antibiotic sensitivity tests showed that the clinical isolates of Salmonella serotype Weltevreden remained drug sensitive but that the vegetable isolates were resistant to at least two antibiotics. To the best of our knowledge, this is the first study to compare clinical and environmental isolates of Salmonella serotype Weltevreden in Malaysia.

Genetic Diversity of Clinical and Environmental Strains of Salmonella enterica Serotype Weltevreden Isolated in Malaysia

Science.gov (United States)

Thong, K. L.; Goh, Y. L.; Radu, S.; Noorzaleha, S.; Yasin, R.; Koh, Y. T.; Lim, V. K. E.; Rusul, G.; Puthucheary, S. D.

2002-01-01

The incidence of food-borne salmonellosis due to Salmonella enterica serotype Weltevreden is reported to be on the increase in Malaysia. The pulsed-field gel electrophoresis (PFGE) subtyping method was used to assess the extent of genetic diversity and clonality of Salmonella serotype Weltevreden strains from humans and the environment. PFGE of XbaI-digested chromosomal DNA from 95 strains of Salmonella serotype Weltevreden gave 39 distinct profiles with a wide range of Dice coefficients (0.27 to 1.00), indicating that PFGE is very discriminative and that multiple clones of Salmonella serotype Weltevreden exist among clinical and environmental isolates. Strains of one dominant pulsotype (pulsotype X1/X2) appeared to be endemic in this region, as they were consistently recovered from humans with salmonellosis between 1996 and 2001 and from raw vegetables. In addition, the sharing of similar PFGE profiles among isolates from humans, vegetables, and beef provides indirect evidence of the possible transmission of salmonellosis from contaminated raw vegetables and meat to humans. Furthermore, the recurrence of PFGE profile X21 among isolates found in samples of vegetables from one wet market indicated the persistence of this clone. The environment in the wet markets may represent a major source of cross-contamination of vegetables with Salmonella serotype Weltevreden. Antibiotic sensitivity tests showed that the clinical isolates of Salmonella serotype Weltevreden remained drug sensitive but that the vegetable isolates were resistant to at least two antibiotics. To the best of our knowledge, this is the first study to compare clinical and environmental isolates of Salmonella serotype Weltevreden in Malaysia. PMID:12089269

DQ High genotypic diversity among methicillin-resistant Staphylococcus pseudintermedius isolated from canine infections in Denmark

DEFF Research Database (Denmark)

Damborg, Peter; Moodley, Arshnee; Aalbaek, Bent

2016-01-01

genotypic diversity and antimicrobial resistance of clinical MRSP isolates obtained from dogs, including dogs sampled on multiple occasions, in Denmark over a six-year period. For that purpose a total of 46 clinical MRSP isolates obtained from 36 dogs between 2009 and 2014 were subjected to antimicrobial...... susceptibility testing, multilocus-sequence typing (MLST) and SCCmec typing. Results: Twenty-three sequence types were identified with ST71, mostly associated with SCCmec II-III, as the most common occurring in 13 dogs. Among the remaining 33 isolates, 19 belonged to clonal complex (CC) 258 comprising ST258...... resistant and almost all CC258 isolates being susceptible. Sixteen of the 19 CC258 isolates had oxacillin MICs of 0.5 g/L, whereas MICs for CC71 isolates were consistently above 4 g/L. Four of five dogs representing multiple isolates had distinct STs on different sampling events. Conclusions: The overall...

Genetic diversity of the msp-1, msp-2, and glurp genes of Plasmodium falciparum isolates along the Thai-Myanmar borders.

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Congpuong, Kanungnit; Sukaram, Rungniran; Prompan, Yuparat; Dornae, Aibteesam

2014-08-01

To study the genetic diversity at the msp-1, msp-2, and glurp genes of Plasmodium falciparum (P. falciparum) isolates from 3 endemic areas in Thailand: Tak, Kanchanaburi and Ranong provinces. A total of 144 P. falciparum isolates collected prior to treatment during January, 2012 to June, 2013 were genotyped. DNA was extracted; allele frequency and diversity of msp-1, msp-2, and glurp genes were investigated by nested polymerase chain reaction. P. falciparum isolates in this study had high rate of multiple genotypes infection (96.5%) with an overall mean multiplicity of infection of 3.21. The distribution of allelic families of msp-1 was significantly different among isolates from Tak, Kanchanaburi, and Ranong but not for the msp-2. K1 and MAD20 were the predominant allelic families at the msp-1 gene, whereas alleles belonging to 3D7 were more frequent at the msp-2 gene. The glurp gene had the least diverse alleles. Population structure of P. falciparum isolates from Tak and Ranong was quite similar as revealed by the presence of similar proportions of MAD20 and K1 alleles at msp-1 loci, 3D7 and FC27 alleles at msp-2 loci as well as comparable mean MOI. Isolates from Kanchanaburi had different structures; the most prevalent alleles were K1 and RO33. The present study shows that P. falciparum isolates from Tak and Ranong provinces had similar allelic pattern of msp-1 and msp-2 and diversity but different from Kanchanaburi isolates. These allelic variant profiles are valuable baseline data for future epidemiological study of malaria transmission and for continued monitoring of polymorphisms associated with antimalarial drug resistance in these areas.

[Isolation methods and diversity of culturable fecal actinobacteria associated with Panthera tigris tigris in Yunnan Safari Park].

Science.gov (United States)

Cao, Yanru; Jiang, Yi; Li, Youlong; Chen, Xiu; Jin, Rongxian; He, Wenxiang

2012-07-04

We studied the isolation methods and diversity of culturable fecal actinobacteria associated with Panthera tigris tigris by using culture-dependent approaches. Fresh fecal samples of healthy Panthera tigris tigris were collected from Yunnan Safari Park. Pretreatment of the samples, isolation media and inhibitors were tested for actinobacteria isolation. 16S rRNA genes of actinobacteria were sequenced and subjected to phylogenetic analysis. The abundance of culturable actinobacteria was 1.10 x 10(8) cfu/g colony forming units (CFU) per gram of feces (wet weight). We obtained 110 purified cultural actinobacterium strains. The analysis based on 16S rRNA gene sequences showed that these strains were distributed in 10 different families and 12 genera of actinobacteria at least, and most of them were non-filamentous, such as Arthrobacter, Dietzia, Kocuria, Corynebacterium and Microbacterium. Streptomyces was the mainly classical filamentous actinobacteria, and up to 64% of total. Drying and heating up the fecal samples can greatly increase the rate of the actinobacteria. Many kinds of inhibitors and chemical defined media are suitable for isolation of fecal actinobacteria. The culturable actinobacteria are abundant in Panthera tigris tigris feces. Our study found an effective method to isolate animals' fecal actinobacteria and it's useful for studying and exploiting animals' fecal actinobacteria.

Phenotypic and Genetic Diversity of Aeromonas Species Isolated from Fresh Water Lakes in Malaysia.

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Wei Ching Khor

Full Text Available Gram-negative bacilli of the genus Aeromonas are primarily inhabitants of the aquatic environment. Humans acquire this organism from a wide range of food and water sources as well as during aquatic recreational activities. In the present study, the diversity and distribution of Aeromonas species from freshwater lakes in Malaysia was investigated using glycerophospholipid-cholesterol acyltransferase (GCAT and RNA polymerase sigma-factor (rpoD genes for speciation. A total of 122 possible Aeromonas strains were isolated and confirmed to genus level using the API20E system. The clonality of the isolates was investigated using ERIC-PCR and 20 duplicate isolates were excluded from the study. The specific GCAT-PCR identified all isolates as belonging to the genus Aeromonas, in agreement with the biochemical identification. A phylogenetic tree was constructed using the rpoD gene sequence and all 102 isolates were identified as: A. veronii 43%, A. jandaei 37%, A. hydrophila 6%, A. caviae 4%, A. salmonicida 2%, A. media 2%, A. allosaccharophila 1%, A. dhakensis 1% and Aeromonas spp. 4%. Twelve virulence genes were present in the following proportions--exu 96%, ser 93%, aer 87%, fla 83%, enolase 70%, ela 62%, act 54%, aexT 33%, lip 16%, dam 16%, alt 8% and ast 4%, and at least 2 of these genes were present in all 102 strains. The ascV, aexU and hlyA genes were not detected among the isolates. A. hydrophila was the main species containing virulence genes alt and ast either present alone or in combination. It is possible that different mechanisms may be used by each genospecies to demonstrate virulence. In summary, with the use of GCAT and rpoD genes, unambiguous identification of Aeromonas species is possible and provides valuable data on the phylogenetic diversity of the organism.

[New isolation methods and phylogenetic diversity of actinobacteria from hypersaline beach in Aksu].

Science.gov (United States)

Zhang, Yao; Xia, Zhanfeng; Cao, Xinbo; Li, Jun; Zhang, Lili

2013-08-04

We explored 4 new methods to improve the isolation of actinobacterial resources from high salt areas. Optimized media based on 4 new strategies were used for isolating actinobacteria from hypersaline beaches. Glycerin-arginine, trehalose-creatine, glycerol-asparticacid, mannitol-casein, casein-mannitol, mannitol-alanine, chitosan-asparagineand GAUZE' No. 1 were used as basic media. New isolation strategy includes 4 methods: ten-fold dilution culture, simulation of the original environment, actinobacterial culture guided by uncultured molecular technology detected, and reference of actinobacterial media for brackish marine environment. The 16S rRNA genes of the isolates were amplified with bacterial universal primers. The results of 16S rRNA gene sequences were compared with sequences obtained from GenBank databases. We constructed phylogenetic tree with the neighbor-joining method. No actinobacterial strains were isolated by 8 media of control group, while 403 strains were isolated by new strategies. The isolates by new methods were members of 14 genera (Streptomyces, Streptomonospora, Saccharomonospora, Plantactinospora, Nocardia, Amycolatopsis, Glycomyces, Micromonospora, Nocardiopsis, Isoptericola, Nonomuraea, Thermobifida, Actinopolyspora, Actinomadura) of 10 families in 8 suborders. The most abundant and diverse isolates were the two suborders of Streptomycineae (69.96%) and Streptosporangineaesuborder (9.68%) within the phylum Actinobacteria, including 9 potential novel species. New isolation methods significantly improved the actinobacterial culturability of hypersaline areas, and obtained many potential novel species, which provided a new and more effective way to isolate actinobacteria resources in hypersaline environments.

Increase in nontuberculous mycobacteria isolated in Shanghai, China: results from a population-based study.

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Jie Wu

Full Text Available BACKGROUND: In China, the prevalence of nontuberculous mycobacteria (NTM in isolates from mycobacterial culture-positive patients with pulmonary tuberculosis (TB is largely unknown. METHODS: We used conventional biochemical and 16S rRNA gene sequencing to identify species of mycobacteria in specimens from patients suspected of having TB. Drug-susceptibility testing was performed on NTM isolates using the proportion method. We also determined the independent risk factors associated with infection with NTM compared with infection with Mycobacterium tuberculosis. RESULTS: The overall rate of NTM isolated from mycobacterial culture-positive patients was 5.9% in this population, with a significantly increasing trend from 3.0% in 2008 to 8.5% in 2012 (P for trend <0.001. The organism most frequently identified was M. kansasii (45.0%, followed by M. intracellulare (20.8% and M. chelonae/abscessus (14.9%. The overall proportion of isolates resistant to the four first-line anti-TB agents were 64.6% for isoniazid, 77.6% for streptomycin, 63.3% for rifampicin and 75.1% for ethambutol. The risk factors most often associated with NTM infection were older age (P for trend <0.001, being a resident of Shanghai (adjusted odds ratio [aOR], 1.48; 95% CI, 1.10-2.00, having been treated for tuberculosis (aOR, 1.64; 95% CI, 1.18-2.29, having a cavity on chest X-ray (aOR, 1.51; 95% CI, 1.16-1.96, and being sputum smear-negative (aOR, 1.59; 95% CI, 1.16-2.18. CONCLUSIONS: The prevalence of NTM isolated in Shanghai increased between 2008 and 2012, thus clinicians should consider NTM as a possible cause of TB-like disease. Accurate species identification is imperative so that proper treatment can be administered for diseases caused by the diversity of NTM species.

European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures.

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Seth-Smith, H M B; Busó, Leonor Sánchez; Livingstone, M; Sait, M; Harris, S R; Aitchison, K D; Vretou, Evangelia; Siarkou, V I; Laroucau, K; Sachse, K; Longbottom, D; Thomson, N R

2017-05-04

Chlamydia abortus (formerly Chlamydophila abortus) is an economically important livestock pathogen, causing ovine enzootic abortion (OEA), and can also cause zoonotic infections in humans affecting pregnancy outcome. Large-scale genomic studies on other chlamydial species are giving insights into the biology of these organisms but have not yet been performed on C. abortus. Our aim was to investigate a broad collection of European isolates of C. abortus, using next generation sequencing methods, looking at diversity, geographic distribution and genome dynamics. Whole genome sequencing was performed on our collection of 57 C. abortus isolates originating primarily from the UK, Germany, France and Greece, but also from Tunisia, Namibia and the USA. Phylogenetic analysis of a total of 64 genomes shows a deep structural division within the C. abortus species with a major clade displaying limited diversity, in addition to a branch carrying two more distantly related Greek isolates, LLG and POS. Within the major clade, seven further phylogenetic groups can be identified, demonstrating geographical associations. The number of variable nucleotide positions across the sampled isolates is significantly lower than those published for C. trachomatis and C. psittaci. No recombination was identified within C. abortus, and no plasmid was found. Analysis of pseudogenes showed lineage specific loss of some functions, notably with several Pmp and TMH/Inc proteins predicted to be inactivated in many of the isolates studied. The diversity within C. abortus appears to be much lower compared to other species within the genus. There are strong geographical signatures within the phylogeny, indicating clonal expansion within areas of limited livestock transport. No recombination has been identified within this species, showing that different species of Chlamydia may demonstrate different evolutionary dynamics, and that the genome of C. abortus is highly stable.

Genetic diversity of pneumococcal surface protein A in invasive pneumococcal isolates from Korean children, 1991-2016.

Science.gov (United States)

Yun, Ki Wook; Choi, Eun Hwa; Lee, Hoan Jong

2017-01-01

Pneumococcal surface protein A (PspA) is an important virulence factor of pneumococci and has been investigated as a primary component of a capsular serotype-independent pneumococcal vaccine. Thus, we sought to determine the genetic diversity of PspA to explore its potential as a vaccine candidate. Among the 190 invasive pneumococcal isolates collected from Korean children between 1991 and 2016, two (1.1%) isolates were found to have no pspA by multiple polymerase chain reactions. The full length pspA genes from 185 pneumococcal isolates were sequenced. The length of pspA varied, ranging from 1,719 to 2,301 base pairs with 55.7-100% nucleotide identity. Based on the sequences of the clade-defining regions, 68.7% and 49.7% were in PspA family 2 and clade 3/family 2, respectively. PspA clade types were correlated with genotypes using multilocus sequence typing and divided into several subclades based on diversity analysis of the N-terminal α-helical regions, which showed nucleotide sequence identities of 45.7-100% and amino acid sequence identities of 23.1-100%. Putative antigenicity plots were also diverse among individual clades and subclades. The differences in antigenicity patterns were concentrated within the N-terminal 120 amino acids. In conclusion, the N-terminal α-helical domain, which is known to be the major immunogenic portion of PspA, is genetically variable and should be further evaluated for antigenic differences and cross-reactivity between various PspA types from pneumococcal isolates.

GENETIC DIVERSITY OF Vibrio harveyi ISOLATED FROM TIGER PRAWN Penaeus monodon HATCHERIES AND GROW OUT PONDS

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Muliani Muliani

2006-06-01

Full Text Available ibrio harveyi is known as one among the most harmful bacteria infecting tiger prawn at every stage of its life’s. The present research was aimed to reveal the genetic diversity of Vibrio harveyi isolated from tiger prawn (Penaeus monodon culture. The samples of bacteria were collected from hatchery (brood-stock, larvae, natural feed, artemia, and larval rearing water and grow-out (juveniles, water, shrimp, sediment, plankton, crab, mollusc, microalgae, and wild fish.  The taxonomic identification of Vibrio spp.was performed based on the physiological and biochemical characteristic following the isolation by Thiosulphate Citrate Bile-salt Sucrose Agar (TCBSA media. Amplified Ribosomoal DNA Restriction Analysis (ARDRA for 16S-rRNA analysis and Macrorestriction Fragment Length Polymorphism (MLFP analysis using Pulsed Field Gel Electrophoresis (PFGE were applied to reveal the genetic diversity of V. harveyi. According to the taxonomic identification, of 361 isolates of Vibrio spp., 129 isolates (35.7% were identified as V. harveyi. The result of ARDRA analysis showed that the 16S-rRNA gene of V. harveyi digested by RsaI and HhaI enzyme, each generated three and four identical fragments respectively for the all samples. These meaned that ARDRA could not reveal any genetic variation on V. harveyi. The size range of all DNA fragment was less than 500 bp. This result indicated that the high genetic diversity of V. harveyi was revealed by MFLP-PFGE analysis. DNA fragment of V. harveyi was digested by NotI enzyme.

Genetic and Biochemical Diversity of Paenibacillus larvae Isolated from Tunisian Infected Honey Bee Broods

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Chadlia Hamdi

2013-01-01

Full Text Available Paenibacillus larvae is the causative agent of American foulbrood (AFB, a virulent disease of honeybee (Apis mellifera larvae. In Tunisia, AFB has been detected in many beekeeping areas, where it causes important economic losses, but nothing is known about the diversity of the causing agent. Seventy-five isolates of P. larvae, identified by biochemical tests and 16S rRNA gene sequencing, were obtained from fifteen contaminated broods showing typical AFB symptoms, collected in different locations in the northern part of the country. Using BOX-PCR, a distinct profile of P. larvae with respect to related Paenibacillus species was detected which may be useful for its identification. Some P. larvae-specific bands represented novel potential molecular markers for the species. BOX-PCR fingerprints indicated a relatively high intraspecific diversity among the isolates not described previously with several molecular polymorphisms identifying six genotypes on polyacrylamide gel. Polymorphisms were also detected in several biochemical characters (indol production, nitrate reduction, and methyl red and oxidase tests. Contrary to the relatively high intraspecies molecular and phenotypic diversity, the in vivo virulence of three selected P. larvae genotypes did not differ significantly, suggesting that the genotypic/phenotypic differences are neutral or related to ecological aspects other than virulence.

Identification of three new isolates of Tomato spotted wilt virus from different hosts in China: molecular diversity, phylogenetic and recombination analyses.

Science.gov (United States)

Zhang, Zhenjia; Wang, Deya; Yu, Chengming; Wang, Zenghui; Dong, Jiahong; Shi, Kerong; Yuan, Xuefeng

2016-01-14

Destructive diseases caused by Tomato spotted wilt virus (TSWV) have been reported associated with many important plants worldwide. Recently, TSWV was reported to infect different hosts in China. It is of value to clone TSWV isolates from different hosts and examine diversity and evolution among different TSWV isolates in China as well as worldwide. RT-PCR was used to clone the full-length genome (L, M and S segments) of three new isolates of TSWV that infected different hosts (tobacco, red pepper and green pepper) in China. Identity of nucleotide and amino acid sequences among TSWV isolates were analyzed by DNAMAN. MEGA 5.0 was used to construct phylogenetic trees. RDP4 was used to detect recombination events during evolution of these isolates. Whole-genome sequences of three new TSWV isolates in China were determined. Together with other available isolates, 29 RNA L, 62 RNA M and 66 RNA S of TSWV isolates were analyzed for molecular diversity, phylogenetic and recombination events. This analysis revealed that the entire TSWV genome, especially the M and S RNAs, had major variations in genomic size that mainly involve the A-U rich intergenic region (IGR). Phylogenetic analyses on TSWV isolates worldwide revealed evidence for frequent reassortments in the evolution of tripartite negative-sense RNA genome. Significant numbers of recombination events with apparent 5' regional preference were detected among TSWV isolates worldwide. Moreover, TSWV isolates with similar recombination events usually had closer relationships in phylogenetic trees. All five Chinese TSWV isolates including three TSWV isolates of this study and previously reported two isolates can be divided into two groups with different origins based on molecular diversity and phylogenetic analysis. During their evolution, both reassortment and recombination played roles. These results suggest that recombination could be an important mechanism in the evolution of multipartite RNA viruses, even negative

Physics in isolation

International Nuclear Information System (INIS)

Anon.

1986-01-01

In late May, about 330 physicists made their way up to isolated and beautiful Lake Louise high in the Canadian Rockies about 100 miles west of Calgary in a second effort to increase interactions between particle and nuclear physicists. The conference series aims to foster exciting and diverse physics by bringing the different physicists together somewhere which is so isolated that they must interact with each other. The formula worked very well and isolated Lake Louise was a huge success

Physics in isolation

Energy Technology Data Exchange (ETDEWEB)

Anon.

1986-09-15

In late May, about 330 physicists made their way up to isolated and beautiful Lake Louise high in the Canadian Rockies about 100 miles west of Calgary in a second effort to increase interactions between particle and nuclear physicists. The conference series aims to foster exciting and diverse physics by bringing the different physicists together somewhere which is so isolated that they must interact with each other. The formula worked very well and isolated Lake Louise was a huge success.

Crop diversity for yield increase.

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Chengyun Li

2009-11-01

Full Text Available Traditional farming practices suggest that cultivation of a mixture of crop species in the same field through temporal and spatial management may be advantageous in boosting yields and preventing disease, but evidence from large-scale field testing is limited. Increasing crop diversity through intercropping addresses the problem of increasing land utilization and crop productivity. In collaboration with farmers and extension personnel, we tested intercropping of tobacco, maize, sugarcane, potato, wheat and broad bean--either by relay cropping or by mixing crop species based on differences in their heights, and practiced these patterns on 15,302 hectares in ten counties in Yunnan Province, China. The results of observation plots within these areas showed that some combinations increased crop yields for the same season between 33.2 and 84.7% and reached a land equivalent ratio (LER of between 1.31 and 1.84. This approach can be easily applied in developing countries, which is crucial in face of dwindling arable land and increasing food demand.

Diversity of biosurfactant producing microorganisms isolated from soils contaminated with diesel oil.

Science.gov (United States)

Menezes Bento, Fátima; de Oliveira Camargo, Flavio A; Okeke, Benedict C; Frankenberger, William T

2005-01-01

Biosurfactant production is a desirable property of hydrocarbon-degrading microorganisms (HDM). We characterized biosurfactant producing microbial populations from a Long Beach soil, California (USA) and a Hong Kong soil (China), contaminated with diesel oil. A total of 33 hydrocarbon-utilizing microorganisms were isolated from the soils. Twelve isolates and three defined consortia were tested for biosurfactant production and emulsification activity. The highest reduction of surface tension was achieved with a consortium of L1, L2 and L3 isolates from a Long Beach soil (41.4mN m(-1)). Isolate L1 (Acinetobacter junii) displayed the highest reduction of surface tension (46.5 mN m(-1)). The emulsifying capacity evaluated by the E24 emulsification index was highest in the culture of isolate L5 (74%). No substantial emulsification was achieved with the cell-free extracts, indicating that the emulsifying activity was not extracellular. Based on surface tension and the E24 index results, isolates F1, F2, F3, F4, L1, L2, L3 and L4 were identified by 16S rRNA gene sequencing as Bacillus cereus, Bacillus sphaericus, B. fusiformis, Acinetobacter junii, a non-cultured bacterium, Pseudomonas sp. and B. pumilus, respectively. Cluster analyses of 16S rRNA gene sequences of the bacterial isolates revealed 70% similarity amongst hydrocarbon-degrading bacterial community present in both soils. Five isolates (isolates F1, F2, F3, F4 and L4) belong to the Firmicutes order, two isolates (L1 and L3) belong to the Proteobacteria order and one isolate (L2) is an Actinomyces sp. Simpson's index (1 - D) and the Shannon-Weaver index (H) revealed more diversity of HDM in the Hong Kong soil, while evenness (E) and the equitability (J) data indicated that there was not a dominant population. Bacterial isolates displaying substantial potential for production of biosurfactants can be applied in the bioremediation of soils contaminated with petroleum hydrocarbons.

Phenotypic and genetic diversity of chlorine-resistant Methylobacterium strains isolated from various environments.

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Hiraishi, A; Furuhata, K; Matsumoto, A; Koike, K A; Fukuyama, M; Tabuchi, K

1995-01-01

Strains of pink-pigmented facultative methylotrophs which were isolated previously from various environments and assigned tentatively to the genus Methylobacterium were characterized in comparison with authentic strains of previously known species of this genus. Most of the isolates derived from chlorinated water supplies exhibited resistance to chlorine, whereas 29 to 40% of the isolates from air, natural aquatic environments, and clinical materials were chlorine resistant. None of the tested authentic strains of Methylobacterium species obtained from culture collections exhibited chlorine resistance. Numerical analysis of phenotypic profiles showed that the test organisms tested were separated from each other except M. organophilum and M. rhodesianum. The chlorine-resistant isolates were randomly distributed among all clusters. The 16S ribosomal DNA (rDNA) sequence-based phylogenetic analyses showed that representatives of the isolates together with known Methylobacterium species formed a line of descent distinct from that of members of related genera in the alpha-2 subclass of the Proteobacteria and were divided into three subclusters within the Methylobacterium group. These results demonstrate that there is phenotypic and genetic diversity among chlorine-resistant Methylobacterium strains within the genus. PMID:7793931

Phenotypic and genetic diversity of chlorine-resistant Methylobacterium strains isolated from various environments.

Science.gov (United States)

Hiraishi, A; Furuhata, K; Matsumoto, A; Koike, K A; Fukuyama, M; Tabuchi, K

1995-06-01

Strains of pink-pigmented facultative methylotrophs which were isolated previously from various environments and assigned tentatively to the genus Methylobacterium were characterized in comparison with authentic strains of previously known species of this genus. Most of the isolates derived from chlorinated water supplies exhibited resistance to chlorine, whereas 29 to 40% of the isolates from air, natural aquatic environments, and clinical materials were chlorine resistant. None of the tested authentic strains of Methylobacterium species obtained from culture collections exhibited chlorine resistance. Numerical analysis of phenotypic profiles showed that the test organisms tested were separated from each other except M. organophilum and M. rhodesianum. The chlorine-resistant isolates were randomly distributed among all clusters. The 16S ribosomal DNA (rDNA) sequence-based phylogenetic analyses showed that representatives of the isolates together with known Methylobacterium species formed a line of descent distinct from that of members of related genera in the alpha-2 subclass of the Proteobacteria and were divided into three subclusters within the Methylobacterium group. These results demonstrate that there is phenotypic and genetic diversity among chlorine-resistant Methylobacterium strains within the genus.

Use of a Packed-Column Bioreactor for Isolation of Diverse Protease-Producing Bacteria from Antarctic Soil

Science.gov (United States)

Wery, Nathalie; Gerike, Ursula; Sharman, Ajay; Chaudhuri, Julian B.; Hough, David W.; Danson, Michael J.

2003-01-01

Seventy-five aerobic heterotrophs have been isolated from a packed-column bioreactor inoculated with soil from Antarctica. The column was maintained at 10°C and continuously fed with a casein-containing medium to enrich protease producers. Twenty-eight isolates were selected for further characterization on the basis of morphology and production of clearing zones on skim milk plates. Phenotypic tests indicated that the strains were mainly psychrotrophs and presented a high morphological and metabolical diversity. The extracellular protease activities tested were optimal at neutral pH and between 30 and 45°C. 16S ribosomal DNA sequence analyses showed that the bioreactor was colonized by a wide variety of taxons, belonging to various bacterial divisions: α-, β-, and γ-Proteobacteria; the Flexibacter-Cytophaga-Bacteroides group; and high G+C gram-positive bacteria and low G+C gram-positive bacteria. Some strains represent candidates for new species of the genera Chryseobacterium and Massilia. This diversity demonstrates that the bioreactor is an efficient enrichment tool compared to traditional isolation strategies. PMID:12620829

Culture Phenotypes of Genomically and Geographically Diverse Mycobacterium avium subsp. paratuberculosis Isolates from Different Hosts▿

Science.gov (United States)

Whittington, Richard J.; Marsh, Ian B.; Saunders, Vanessa; Grant, Irene R.; Juste, Ramon; Sevilla, Iker A.; Manning, Elizabeth J. B.; Whitlock, Robert H.

2011-01-01

Mycobacterium avium subsp. paratuberculosis causes paratuberculosis (Johne's disease) in ruminants in most countries. Historical data suggest substantial differences in culturability of M. avium subsp. paratuberculosis isolates from small ruminants and cattle; however, a systematic comparison of culture media and isolates from different countries and hosts has not been undertaken. Here, 35 field isolates from the United States, Spain, Northern Ireland, and Australia were propagated in Bactec 12B medium and Middlebrook 7H10 agar, genomically characterized, and subcultured to Lowenstein-Jensen (LJ), Herrold's egg yolk (HEY), modified Middlebrook 7H10, Middlebrook 7H11, and Watson-Reid (WR) agars, all with and without mycobactin J and some with sodium pyruvate. Fourteen genotypes of M. avium subsp. paratuberculosis were represented as determined by BstEII IS900 and IS1311 restriction fragment length polymorphism analysis. There was no correlation between genotype and overall culturability, although most S strains tended to grow poorly on HEY agar. Pyruvate was inhibitory to some isolates. All strains grew on modified Middlebrook 7H10 agar but more slowly and less prolifically on LJ agar. Mycobactin J was required for growth on all media except 7H11 agar, but growth was improved by the addition of mycobactin J to 7H11 agar. WR agar supported the growth of few isolates. The differences in growth of M. avium subsp. paratuberculosis that have historically been reported in diverse settings have been strongly influenced by the type of culture medium used. When an optimal culture medium, such as modified Middlebrook 7H10 agar, is used, very little difference between the growth phenotypes of diverse strains of M. avium subsp. paratuberculosis was observed. This optimal medium is recommended to remove bias in the isolation and cultivation of M. avium subsp. paratuberculosis. PMID:21430104

Increasing Diversity in Emerging Non-religious Communities

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Christopher Hassall

2014-12-01

Full Text Available Contemporary growth in non-religious populations has given rise to novel communities with unique perspectives on social issues. We describe a study of diversity within speakers at conferences organised by and attended by the atheist community. We analyse trends in diversity of 630 speakers, corresponding to 1223 speaking slots at 48 conferences conducted for the purpose of discussing or espousing non-religious views over the period 2003–2014. Diversity among speakers (defined using multivariate statistics in terms of the representation of women and non-white people increased significantly over time during the period studied. This broadening participation may have arisen from interventions to address issues of representation or may simply reflect a generational shift in the demographics of the community. However, on-going problems with data collection and the imbalance in the social cost of identifying as non-religious between different social groups continue to impede efforts to reduce barriers to equality within this growing movement.

Characterization of the repertoire diversity of the Plasmodium falciparum stevor multigene family in laboratory and field isolates

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Holder Anthony A

2009-06-01

Full Text Available Abstract Background The evasion of host immune response by the human malaria parasite Plasmodium falciparum has been linked to expression of a range of variable antigens on the infected erythrocyte surface. Several genes are potentially involved in this process with the var, rif and stevor multigene families being the most likely candidates and coding for rapidly evolving proteins. The high sequence diversity of proteins encoded by these gene families may have evolved as an immune evasion strategy that enables the parasite to establish long lasting chronic infections. Previous findings have shown that the hypervariable region (HVR of STEVOR has significant sequence diversity both within as well as across different P. falciparum lines. However, these studies did not address whether or not there are ancestral stevor that can be found in different parasites. Methods DNA and RNA sequences analysis as well as phylogenetic approaches were used to analyse the stevor sequence repertoire and diversity in laboratory lines and Kilifi (Kenya fresh isolates. Results Conserved stevor genes were identified in different P. falciparum isolates from different global locations. Consistent with previous studies, the HVR of the stevor gene family was found to be highly divergent both within and between isolates. Importantly phylogenetic analysis shows some clustering of stevor sequences both within a single parasite clone as well as across different parasite isolates. Conclusion This indicates that the ancestral P. falciparum parasite genome already contained multiple stevor genes that have subsequently diversified further within the different P. falciparum populations. It also confirms that STEVOR is under strong selection pressure.

Genetic diversity and virulence potential of Staphylococcus aureus isolates from raw and processed food commodities in Shanghai.

Science.gov (United States)

Song, Minghui; Bai, Yalong; Xu, Jie; Carter, Michelle Qiu; Shi, Chunlei; Shi, Xianming

2015-02-16

The risk of zoonotic transmission to humans highlights the need to understand the molecular ecology of Staphylococcus aureus in foods. In this study, 142 S. aureus isolates obtained from various raw and processed foods from Shanghai, China were characterized to determine their genetic diversity and virulence gene content. A total of 16 clonal complexes (CCs), 34 staphylococcal protein A (spa) types, and 6 accessory gene regulator (agr) allelic groups were identified and analyzed among the 142 S. aureus isolates. Among these, the genotype CC188-t189-agr Ι was the most prevalent, constituting 28.2% of all isolates. The presence of virulence genes encoding 20 staphylococcal enterotoxins (se), toxic shock syndrome toxin (tsst1), exfoliative toxins (eta, etb, and etd), Panton-Valentine leukocidin (lukS-PV and lukF-PV), as well as methicillin resistance gene (mecA), was determined by PCR. Of these S. aureus isolates, 72.5% harbored toxin genes, in which the most frequent toxin gene was sep (43.7%), followed by sej (26.1%) and pvl (21.1%). In contrast, see, ses, set, tsst1, etb, and etd were not found in any of the isolates tested. Eight S. aureus isolates (5.6%, 8/142), seven from raw milk and one from frozen food, were mecA positive and resistant to oxacillin, thus were MRSA. The 142 S. aureus isolates displayed 52 different toxin gene profiles. Although no direct association was found between toxin gene profile and the S. aureus genotype, the isolates belonging to CC5, CC9, CC20, CC50, and CC72 clonal lineages in general carried more toxin genes (>5) compared with the isolates in other CCs. It was also revealed that raw milk and raw meat were the major sources of isolates containing multiple toxin genes. S. aureus isolates from food that were genetically highly related, displayed diverse toxin gene profiles, implying the significant role of horizontal gene transfer in the emergence of highly toxigenic S. aureus isolates. Copyright © 2014 Elsevier B.V. All rights

MIRU-VNTR genotype diversity and indications of homoplasy in M. avium strains isolated from humans and slaughter pigs in Latvia.

Science.gov (United States)

Kalvisa, Adrija; Tsirogiannis, Constantinos; Silamikelis, Ivars; Skenders, Girts; Broka, Lonija; Zirnitis, Agris; Jansone, Inta; Ranka, Renate

2016-09-01

Diseases which are caused by non-tuberculous mycobacteria (NTM) are an increasing problem in the developed countries. In Latvia, one of the most clinically important members of NTM is Mycobacterium avium (M. avium), an opportunistic pathogen which has been isolated from several lung disease patients and tissue samples of slaughter pigs. This study was designed to characterize the genetic diversity of the M. avium isolates in Latvia and to compare the distribution of genotypic patterns among humans and pigs. Eleven (Hall and Salipante, 2010) clinical M. avium samples, isolated from patients of Center of Tuberculosis and Lung Diseases (years 2003-2010), and 32 isolates from pig necrotic mesenterial lymph nodes in different regions (years 2003-2007) were analyzed. The majority (42 of 43) of samples were identified as M. avium subsp. hominissuis; one porcine isolate belonged to M. avium subsp. avium. MIRU-VNTR genotyping revealed 13 distinct genotypes, among which nine genotype patterns, including M. avium subsp. avium isolate, were newly identified. IS1245 RFLP fingerprinting of 25 M. avium subsp. hominissuis samples yielded 17 different IS1245 RFLP patterns, allowing an efficient discrimination of isolates. Clusters of identical RFLP profiles were observed within host species, geographical locations and time frame of several years. Additional in silico analysis on simulated MIRU-VNTR genotype population datasets showed that the MIRU-VNTR pattern similarity could partly arise due to probabilistic increase of acquiring homoplasy among subpopulations, thus the similar MIRU-VNTR profiles of M. avium strains even in close geographical proximity should be interpreted with caution. Copyright © 2016 Elsevier B.V. All rights reserved.

Diversity of Paenibacillus polymyxa strains isolated from the rhizosphere of maize planted in Cerrado soil

NARCIS (Netherlands)

Weid, von der I.; Paiva, E.; Nobrega, A.; Elsas, van J.D.; Seldin, L.

2000-01-01

Paenibacillus polymyxa populations present in the rhizosphere of maize (cultivar BR-201) planted in Cerrado soil were investigated in order to assess their diversity at four stages of plant growth. A total of 67 strains were isolated and all strains were identified as P. polymyxa by classical

Diversity and Geographical Distribution of Flavobacterium psychrophilum Isolates and Their Phages: Patterns of Susceptibility to Phage Infection and Phage Host Range

DEFF Research Database (Denmark)

Castillo, Daniel; Christiansen, Rói Hammershaimb; Espejo, Romilio

2014-01-01

in disease control requires detailed knowledge about the diversity and dynamics of host susceptibility to phage infection. For this reason, we examined the genetic diversity of 49 F. psychrophilum strains isolated in three different areas (Chile, Denmark, and USA) through direct genome restriction enzyme...... analysis (DGREA) and their susceptibility to 33 bacteriophages isolated in Chile and Denmark, thus covering large geographical (>12,000 km) and temporal (>60 years) scales of isolation. An additional 40 phage-resistant isolates obtained from culture experiments after exposure to specific phages were...... examined for changes in phage susceptibility against the 33 phages. The F. psychrophilum and phage populations isolated from Chile and Denmark clustered into geographically distinct groups with respect to DGREA profile and host range, respectively. However, cross infection between Chilean phage isolates...

Plant growth promoting capability and genetic diversity of bacteria isolated from mud volcano and lime cave of Andaman and Nicobar Islands.

Science.gov (United States)

Venkadesaperumal, Gopu; Amaresan, Natrajan; Kumar, Krishna

2014-01-01

Twenty four bacterial strains from four different regions of mud volcano and lime cave were isolated to estimate their diversity, plant growth promoting and biocontrol activities to use them as inoculant strains in the fields. An excellent antagonistic effect against four plant pathogens and plant growth promoting properties such as IAA production, HCN production, phosphate solubilization, siderophore production, starch hydrolysis and hydrolytic enzymes syntheses were identified in OM5 (Pantoea agglomerans) and EM9 (Exiguobacterium sp.) of 24 studied isolates. Seeds (Chili and tomato) inoculation with plant growth promoting strains resulted in increased percentage of seedling emergence, root length and plant weight. Results indicated that co-inoculation gave a more pronounced effects on seedling emergence, secondary root numbers, primary root length and stem length, while inoculation by alone isolate showed a lower effect. Our results suggest that the mixed inocula of OM5 and EM9 strains as biofertilizers could significantly increase the production of food crops in Andaman archipelago by means of sustainable and organic agricultural system.

Plant growth promoting capability and genetic diversity of bacteria isolated from mud volcano and lime cave of Andaman and Nicobar Islands

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Gopu Venkadesaperumal

2014-12-01

Full Text Available Twenty four bacterial strains from four different regions of mud volcano and lime cave were isolated to estimate their diversity, plant growth promoting and biocontrol activities to use them as inoculant strains in the fields. An excellent antagonistic effect against four plant pathogens and plant growth promoting properties such as IAA production, HCN production, phosphate solubilization, siderophore production, starch hydrolysis and hydrolytic enzymes syntheses were identified in OM5 (Pantoea agglomerans and EM9 (Exiguobacterium sp. of 24 studied isolates. Seeds (Chili and tomato inoculation with plant growth promoting strains resulted in increased percentage of seedling emergence, root length and plant weight. Results indicated that co-inoculation gave a more pronounced effects on seedling emergence, secondary root numbers, primary root length and stem length, while inoculation by alone isolate showed a lower effect. Our results suggest that the mixed inocula of OM5 and EM9 strains as biofertilizers could significantly increase the production of food crops in Andaman archipelago by means of sustainable and organic agricultural system.

Functional Characterization of Bacteria Isolated from Ancient Arctic Soil Exposes Diverse Resistance Mechanisms to Modern Antibiotics

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Perron, Gabriel G.; Whyte, Lyle; Turnbaugh, Peter J.; Goordial, Jacqueline; Hanage, William P.; Dantas, Gautam; Desai, Michael M.

2015-01-01

Using functional metagenomics to study the resistomes of bacterial communities isolated from different layers of the Canadian high Arctic permafrost, we show that microbial communities harbored diverse resistance mechanisms at least 5,000 years ago. Among bacteria sampled from the ancient layers of a permafrost core, we isolated eight genes conferring clinical levels of resistance against aminoglycoside, β-lactam and tetracycline antibiotics that are naturally produced by microorganisms. Among these resistance genes, four also conferred resistance against amikacin, a modern semi-synthetic antibiotic that does not naturally occur in microorganisms. In bacteria sampled from the overlaying active layer, we isolated ten different genes conferring resistance to all six antibiotics tested in this study, including aminoglycoside, β-lactam and tetracycline variants that are naturally produced by microorganisms as well as semi-synthetic variants produced in the laboratory. On average, we found that resistance genes found in permafrost bacteria conferred lower levels of resistance against clinically relevant antibiotics than resistance genes sampled from the active layer. Our results demonstrate that antibiotic resistance genes were functionally diverse prior to the anthropogenic use of antibiotics, contributing to the evolution of natural reservoirs of resistance genes. PMID:25807523

Nitrogen addition, not initial phylogenetic diversity, increases litter decomposition by fungal communities.

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Amend, Anthony S; Matulich, Kristin L; Martiny, Jennifer B H

2015-01-01

Fungi play a critical role in the degradation of organic matter. Because different combinations of fungi result in different rates of decomposition, determining how climate change will affect microbial composition and function is fundamental to predicting future environments. Fungal response to global change is patterned by genetic relatedness, resulting in communities with comparatively low phylogenetic diversity (PD). This may have important implications for the functional capacity of disturbed communities if lineages sensitive to disturbance also contain unique traits important for litter decomposition. Here we tested the relationship between PD and decomposition rates. Leaf litter fungi were isolated from the field and deployed in microcosms as mock communities along a gradient of initial PD, while species richness was held constant. Replicate communities were subject to nitrogen fertilization comparable to anthropogenic deposition levels. Carbon mineralization rates were measured over the course of 66 days. We found that nitrogen fertilization increased cumulative respiration by 24.8%, and that differences in respiration between fertilized and ambient communities diminished over the course of the experiment. Initial PD failed to predict respiration rates or their change in response to nitrogen fertilization, and there was no correlation between community similarity and respiration rates. Last, we detected no phylogenetic signal in the contributions of individual isolates to respiration rates. Our results suggest that the degree to which PD predicts ecosystem function will depend on environmental context.

Comparison of chickpea rhizobia isolates from diverse Portuguese natural populations based on symbiotic effectiveness and DNA fingerprint.

Science.gov (United States)

Laranjo, M; Branco, C; Soares, R; Alho, L; Carvalho, M D E; Oliveira, S

2002-01-01

To test the hypothesis that differences in chickpea yields obtained in four distinct Portuguese regions (Beja, Elvas-Casas Velhas, Elvas-Estação Nacional de Melhoramento de Plantas (ENMP) and Evora) could be due to variation between the natural rhizobia populations. Estimation of the size of the different rhizobial populations showed that Elvas-ENMP population was the largest one. Elvas-ENMP population also revealed a higher proportion of isolates carrying more than one plasmid. Assessment of genetic diversity of the native rhizobia populations by a DNA fingerprinting PCR method, here designated as DAPD (Direct Amplified Polymorphic DNA), showed a higher degree of variation in Elvas-ENMP and Beja populations. The symbiotic effectiveness (SE) of 39 isolates was determined and ranged 13-34%. Statistical analysis showed that SE was negatively correlated with plasmid number of the isolate. The largest indigenous rhizobia population was found in Elvas-ENMP. DAPD pattern and plasmid profile analysis both suggested a higher genetic diversity among the populations of Elvas-ENMP and Beja. No relationship was found between SE of the isolates and their origin site. The large native population, rather than the symbiotic performance of individual rhizobia, could contribute to the higher chickpea yields obtained in Elvas-ENMP.

Diversity of Antifungal Compounds-Producing Bacillus spp. Isolated from Rhizosphere of Soybean Plant Based on ARDRA and 16S rRNA

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ARIS TRI WAHYUDI

2010-09-01

Full Text Available Plant growth promoting rhizobacteria (PGPR play an important role in improvement of seed germination, root development, and water utilization by plants. These rhizobacteria can stimulate plant growth directly by producing growth hormones or indirectly by producing antifungal compounds/antibiotics to suppress phytopathogenic fungi. The objective of this research was to analyze the diversity of 22 antifungal-producing rhizobacteria of Bacillus sp. isolated from rhizosphere of soybean plant based on Amplified rDNA Restriction Analysis (ARDRA and 16S rRNA Sequence. Restriction enzymes in ARDRA analysis, HinfI, HaeIII, and RsaI were used to digest 22 16S rDNA amplified from Bacillus sp. genomes. Based on this analysis, genetic diversity of 22 Bacillus sp. producing antifungal compounds were classified into eight different groups. Moreover, six selected isolates randomly from each ARDRA group that have strong activity to suppress fungal growth were analyzed for their 16S rDNA sequences compared with reference strains. The distributions of these isolates were genetically diverse on several species of Bacillus sp. such as B. subtilis, B. cereus, and B. fusiformis. ARDRA is a reliable technique to analyze genetic diversity of Bacillus sp. community in the rhizosphere.

Diversity of bacteria associated with Bursaphelenchus xylophilus and other nematodes isolated from Pinus pinaster trees with pine wilt disease.

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Proença, Diogo Neves; Francisco, Romeu; Santos, Clara Vieira; Lopes, André; Fonseca, Luís; Abrantes, Isabel M O; Morais, Paula V

2010-12-09

The pinewood nematode (PWN), Bursaphelenchus xylophilus, has been thought to be the only causal agent of pine wilt disease (PWD), however, since bacteria have been suggested to play a role in PWD, it is important to know the diversity of the microbial community associated to it. This study aimed to assess the microbial community associated with B. xylophilus and with other nematodes isolated from pine trees, Pinus pinaster, with PWD from three different affected forest areas in Portugal. One hundred and twenty three bacteria strains were isolated from PWN and other nematodes collected from 14 P. pinaster. The bacteria strains were identified by comparative analysis of the 16S rRNA gene partial sequence. All except one gram-positive strain (Actinobacteria) belonged to the gram-negative Beta and Gammaproteobacteria. Most isolates belonged to the genus Pseudomonas, Burkholderia and to the family Enterobacteriaceae. Species isolated in higher percentage were Pseudomonas lutea, Yersinia intermedia and Burkholderia tuberum. The major bacterial population associated to the nematodes differed according to the forest area and none of the isolated bacterial species was found in all different forest areas. For each of the sampled areas, 60 to 100% of the isolates produced siderophores and at least 40% produced lipases. The ability to produce siderophores and lipases by most isolates enables these bacteria to have a role in plant physiological response. This research showed a high diversity of the microbial community associated with B. xylophilus and other nematodes isolated from P. pinaster with PWD.

Genomic Diversity of Lactobacillus salivarius▿ †

OpenAIRE

Raftis, Emma J.; Salvetti, Elisa; Torriani, Sandra; Felis, Giovanna E.; O'Toole, Paul W.

2010-01-01

Strains of Lactobacillus salivarius are increasingly employed as probiotic agents for humans or animals. Despite the diversity of environmental sources from which they have been isolated, the genomic diversity of L. salivarius has been poorly characterized, and the implications of this diversity for strain selection have not been examined. To tackle this, we applied comparative genomic hybridization (CGH) and multilocus sequence typing (MLST) to 33 strains derived from humans, animals, or foo...

Diversity of seM in Streptococcus equi subsp. equi isolated from strangles outbreaks.

Science.gov (United States)

Libardoni, Felipe; Vielmo, Andréia; Farias, Luana; Matter, Letícia Beatriz; Pötter, Luciana; Spilki, Fernando Rosado; de Vargas, Agueda Castagna

2013-03-23

Strangles is the main upper respiratory tract disease of horses. There are currently no studies on the changes in alleles of the M protein gene (seM) in Brazilian isolates of Streptococcus equi ssp. equi (S. equi). This study aimed to analyze and differentiate molecularly S. equi isolates from equine clinical specimens from southern Brazil, between 1994 and 2010. seM alleles were analyzed in 47 isolates of S. equi obtained from clinical cases of strangles (15 Thoroughbred horses, 29 Crioulo breed horses and three Brasileiro de Hipismo--BH). seM alleles characterization was performed by comparing variable region sequences of the seM gene. The alleles were also phylogenetically grouped by Neighbor-joining analysis, which demonstrated the geographic distribution of those in properties from southern Brazil. Fifteen alleles of the gene seM were found among the 47 S. equi isolates analyzed. Among these, only one allele (seM-61), which was identified in seven isolates (14.9%), was found in the database PubMLST-seM. Within the new alleles, allele seM-115 was the most prevalent, having been found in 13 isolates (27.7%), followed by allele seM-117 in 10 isolates (21.3%). In the Brazilian horse population studied, there is greater diversity of M protein alleles in S. equi isolates compared to worldwide data deposited in PubMLST-seM. Among the 15 seM alleles identified, only one allele sequence was previously published. The alleles identification is important to control the disease by guiding selection of strains for the manufacture of commercial and autogenous vaccines. Copyright © 2012 Elsevier B.V. All rights reserved.

[Diversity and bioactivity analysis of actinomycetes isolated from grand Shangri-La soil].

Science.gov (United States)

Cao, Yanru; Jiang, Yi; Xu, Lihua

2009-01-01

To obtain new pharmaceuticals and enzymes with high activity,we studied the composition as well as antimicrobial and enzyme activities of actinomycetes in Grand Shangri-La. Using 4 media,we isolated mesophilic and psychrophilic actinomycetes from 220 soil samples collected from areas with different altitudes in Grand Shangri-La. Twenty-five representative isolates were phylogenetically analyzed based on their 16S rRNA gene sequences. Antimicrobial activities against four bacteria and seven fungi were tested using agar well diffusion method. Genes encoding type I and II polyketide synthases (PKS I, PKS II), nonribosomal peptide synthase (NRPS) and polyene cytochrome P450 hydroxylase (CYP) were screened by PCR. Furthermore,several enzyme activities of psychrophilic actinomycetes were examined. The 25 representative strains belonged to 6 suborders, 12 families and 15 genera of the order Actinomycetals. For NRPS and CYP genes screening, positive strains were 14 and 11, respectively. Among the 111 actinomycetes isolated under low-temperature conditions, 88% were psychrotroph strains, 12% were psychrophilic actinomycetes, and most of them utilized gelatin, cellulose and chitin. Actinomycetes diversity is rich in Grand Shangri-la, and has the potential for conservation and utilization of actinomycetes resources.

Diversity and functional properties of acid-tolerant bacteria isolated from tea plantation soil of Assam.

Science.gov (United States)

Goswami, Gunajit; Deka, Priyadarshini; Das, Pompi; Bora, Sudipta Sankar; Samanta, Ramkrishna; Boro, Robin Chandra; Barooah, Madhumita

2017-07-01

In this study, we report on the bacterial diversity and their functional properties prevalent in tea garden soils of Assam that have low pH (3.8-5.5). Culture-dependent studies and phospholipid fatty acid analysis revealed a high abundance of Gram-positive bacteria. Further, 70 acid-tolerant bacterial isolates characterized using a polyphasic taxonomy approach could be grouped to the genus Bacillus, Lysinibacillus, Staphylococcus, Brevundimonas, Alcaligenes, Enterobacter, Klebsiella, Escherichia, and Aeromonas. Among the 70 isolates, 47 most promising isolates were tested for their plant growth promoting activity based on the production of Indole Acetic Acid (IAA), siderophore, and HCN as well as solubilization of phosphate, zinc, and potassium. Out of the 47 isolates, 10 isolates tested positive for the entire aforesaid plant growth promoting tests and further tested for quantitative analyses for production of IAA, siderophore, and phosphate solubilization at the acidic and neutral condition. Results indicated that IAA and siderophore production, as well as phosphate solubilization efficiency of the isolates decreased significantly (P ≤ 0.05) in the acidic environment. This study revealed that low soil pH influences bacterial community structure and their functional properties.

Diversity and antimicrobial activity of culturable endophytic fungi isolated from moso bamboo seeds.

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Xiao-Ye Shen

Full Text Available Bamboos, regarded as therapeutic agents in ethnomedicine, have been used to inhibit inflammation and enhance natural immunity for a long time in Asia, and there are many bamboo associated fungi with medical and edible value. In the present study, a total of 350 fungal strains were isolated from the uncommon moso bamboo (Phyllostachys edulis seeds for the first time. The molecular diversity of these endophytic fungi was investigated and bioactive compound producers were screened for the first time. All the fungal endophytes were categorized into 69 morphotypes according to culturable characteristics and their internal transcriber spacer (ITS regions were analyzed by BLAST search with the NCBI database. The fungal isolates showed high diversity and were divided in Ascomycota (98.0% and Basidiomycota (2.0%, including at least 19 genera in nine orders. Four particular genera were considered to be newly recorded bambusicolous fungi, including Leptosphaerulina, Simplicillium, Sebacina and an unknown genus in Basidiomycetes. Furthermore, inhibitory effects against clinical pathogens and phytopathogens were screened preliminarily and strains B09 (Cladosporium sp., B34 (Curvularia sp., B35 (undefined genus 1, B38 (Penicillium sp. and zzz816 (Shiraia sp. displayed broad-spectrum activity against clinical bacteria and yeasts by the agar diffusion method. The crude extracts of isolates B09, B34, B35, B38 and zzz816 under submerged fermentation, also demonstrated various levels of bioactivities against bambusicolous pathogenic fungi. This study is the first report on the antimicrobial activity of endophytic fungi associated with moso bamboo seeds, and the results show that they could be exploited as a potential source of bioactive compounds and plant defense activators. In addition, it is the first time that strains of Shiraia sp. have been isolated and cultured from moso bamboo seeds, and one of them (zzz816 could produce hypocrellin A at high yield, which

Purpose in life as a resource for increasing comfort with ethnic diversity.

Science.gov (United States)

Burrow, Anthony L; Stanley, Maclen; Sumner, Rachel; Hill, Patrick L

2014-11-01

Emerging demographic trends signal that White Americans will soon relinquish their majority status. As Whites' acclimation to an increasingly diverse society is poised to figure prominently in their adjustment, identifying sources of greater comfort with diversity is important. Three studies (N = 519) revealed evidence that purpose in life bolsters comfort with ethnic diversity among White adults. Specifically, dispositional purpose was positively related to diversity attitudes and attenuated feelings of threat resulting from viewing demographic projections of greater diversity. In addition, when primed experimentally, purpose attenuated participants' preferences for living in an ethnically homogeneous-White city, relative to a more diverse city when shown maps displaying ethno-demographic information. These effects persisted after controlling for positive affect and perceived connections to ethnic out-groups, suggesting the robust influence of purpose. Potential benefits of situating purpose as a unique resource for navigating an increasingly diverse society are discussed. © 2014 by the Society for Personality and Social Psychology, Inc.

Isolation of diverse members of the Aquificales from geothermal springs in Tengchong, China.

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Hedlund, Brian P; Reysenbach, Anna-Louise; Huang, Liuquin; Ong, John C; Liu, Zizhang; Dodsworth, Jeremy A; Ahmed, Reham; Williams, Amanda J; Briggs, Brandon R; Liu, Yitai; Hou, Weiguo; Dong, Hailiang

2015-01-01

The order Aquificales (phylum Aquificae) consists of thermophilic and hyperthermophilic bacteria that are prominent in many geothermal systems, including those in Tengchong, Yunnan Province, China. However, Aquificales have not previously been isolated from Tengchong. We isolated five strains of Aquificales from diverse springs (temperature 45.2-83.3°C and pH 2.6-9.1) in the Rehai Geothermal Field from sites in which Aquificales were abundant. Phylogenetic analysis showed that four of the strains belong to the genera Hydrogenobacter, Hydrogenobaculum, and Sulfurihydrogenibium, including strains distant enough to likely justify new species of Hydrogenobacter and Hydrogenobaculum. The additional strain may represent a new genus in the Hydrogenothermaceae. All strains were capable of aerobic respiration under microaerophilic conditions; however, they had variable capacity for chemolithotrophic oxidation of hydrogen and sulfur compounds and nitrate reduction.

Diversity and antimicrobial resistance of Salmonella enterica isolates from surface water in Southeastern United States.

Science.gov (United States)

Li, Baoguang; Vellidis, George; Liu, Huanli; Jay-Russell, Michele; Zhao, Shaohua; Hu, Zonglin; Wright, Anita; Elkins, Christopher A

2014-10-01

A study of prevalence, diversity, and antimicrobial resistance of Salmonella enterica in surface water in the southeastern United States was conducted. A new scheme was developed for recovery of Salmonella from irrigation pond water and compared with the FDA's Bacteriological Analytical Manual (8th ed., 2014) (BAM) method. Fifty-one isolates were recovered from 10 irrigation ponds in produce farms over a 2-year period; nine Salmonella serovars were identified by pulsed-field gel electrophoresis analysis, and the major serovar was Salmonella enterica serovar Newport (S. Newport, n = 29), followed by S. enterica serovar Enteritidis (n = 6), S. enterica serovar Muenchen (n = 4), S. enterica serovar Javiana (n = 3), S. enterica serovar Thompson (n = 2), and other serovars. It is noteworthy that the PulseNet patterns of some of the isolates were identical to those of the strains that were associated with the S. Thompson outbreaks in 2010, 2012, and 2013, S. Enteritidis outbreaks in 2011 and 2013, and an S. Javiana outbreak in 2012. Antimicrobial susceptibility testing confirmed 16 S. Newport isolates of the multidrug resistant-AmpC (MDR-AmpC) phenotype, which exhibited resistance to ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline (ACSSuT), and to the 1st, 2nd, and 3rd generations of cephalosporins (cephalothin, amoxicillin-clavulanic acid, and ceftriaxone). Moreover, the S. Newport MDR-AmpC isolates had a PFGE pattern indistinguishable from the patterns of the isolates from clinical settings. These findings suggest that the irrigation water may be a potential source of contamination of Salmonella in fresh produce. The new Salmonella isolation scheme significantly increased recovery efficiency from 21.2 (36/170) to 29.4% (50/170) (P = 0.0002) and streamlined the turnaround time from 5 to 9 days with the BAM method to 4 days and thus may facilitate microbiological analysis of environmental water. Copyright © 2014, American Society for

Genetic diversity and population structure of Lactobacillus delbrueckii subspecies bulgaricus isolated from naturally fermented dairy foods.

Science.gov (United States)

Song, Yuqin; Sun, Zhihong; Guo, Chenyi; Wu, Yarong; Liu, Wenjun; Yu, Jie; Menghe, Bilige; Yang, Ruifu; Zhang, Heping

2016-03-04

Lactobacillus delbrueckii subsp. bulgaricus is one of the most widely used starter culture strains in industrial fermented dairy manufacture. It is also common in naturally fermented dairy foods made using traditional methods. The subsp. bulgaricus strains found in naturally fermented foods may be useful for improving current industrial starter cultures; however, little is known regarding its genetic diversity and population structure. Here, a collection of 298 L. delbrueckii strains from naturally fermented products in Mongolia, Russia, and West China was analyzed by multi-locus sequence typing based on eight conserved genes. The 251 confirmed subsp. bulgaricus strains produced 106 unique sequence types, the majority of which were assigned to five clonal complexes (CCs). The geographical distribution of CCs was uneven, with CC1 dominated by Mongolian and Russian isolates, and CC2-CC5 isolates exclusively from Xinjiang, China. Population structure analysis suggested six lineages, L1-L6, with various homologous recombination rates. Although L2-L5 were mainly restricted within specific regions, strains belonging to L1 and L6 were observed in diverse regions, suggesting historical transmission events. These results greatly enhance our knowledge of the population diversity of subsp. bulgaricus strains, and suggest that strains from CC1 and L4 may be useful as starter strains in industrial fermentation.

Diversity of bacteria associated with Bursaphelenchus xylophilus and other nematodes isolated from Pinus pinaster trees with pine wilt disease.

Directory of Open Access Journals (Sweden)

Diogo Neves Proença

Full Text Available The pinewood nematode (PWN, Bursaphelenchus xylophilus, has been thought to be the only causal agent of pine wilt disease (PWD, however, since bacteria have been suggested to play a role in PWD, it is important to know the diversity of the microbial community associated to it. This study aimed to assess the microbial community associated with B. xylophilus and with other nematodes isolated from pine trees, Pinus pinaster, with PWD from three different affected forest areas in Portugal. One hundred and twenty three bacteria strains were isolated from PWN and other nematodes collected from 14 P. pinaster. The bacteria strains were identified by comparative analysis of the 16S rRNA gene partial sequence. All except one gram-positive strain (Actinobacteria belonged to the gram-negative Beta and Gammaproteobacteria. Most isolates belonged to the genus Pseudomonas, Burkholderia and to the family Enterobacteriaceae. Species isolated in higher percentage were Pseudomonas lutea, Yersinia intermedia and Burkholderia tuberum. The major bacterial population associated to the nematodes differed according to the forest area and none of the isolated bacterial species was found in all different forest areas. For each of the sampled areas, 60 to 100% of the isolates produced siderophores and at least 40% produced lipases. The ability to produce siderophores and lipases by most isolates enables these bacteria to have a role in plant physiological response. This research showed a high diversity of the microbial community associated with B. xylophilus and other nematodes isolated from P. pinaster with PWD.

Genetic Diversity of Some Tunisian Botrytis cinerea Isolates Using Molecular Markers

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D. ben Ahmed

2005-12-01

Full Text Available The genetic diversity of Botrytis cinerea in Tunisia was studied using molecular markers, and the level of resistance to the fungicide fenhexamid was shown. Isolates from different plants (grape, tomato, cucumber, onion, strawberry, gerbera and rose and different parts of the country were analysed in order to determine whether the two groups, transposa and vacuma, that were detected in French vineyards, are also present in Tunisia. A combined PCR and Dot Blot method was developed to identify the transposable elements Boty and Flipper that distinguish between these two B. cinerea groups. Both the transposa and vacuma groups, and isolates containing the transposable element Boty, were found in Tunisia. Moreover, analysis of the Bc-hch locus by PCR and restriction enzyme digestion identified only the B. cinerea group corresponding to one allelic type. Finally, by using the level of resistance shown by B. cinerea to the fungicide fenhexamid as a marker, it was confirmed that this was the only group of B. cinerea in the Tunisian population.

Virulence genes and genetic diversity of Streptococcus suis serotype 2 isolates from Thailand.

Science.gov (United States)

Maneerat, K; Yongkiettrakul, S; Kramomtong, I; Tongtawe, P; Tapchaisri, P; Luangsuk, P; Chaicumpa, W; Gottschalk, M; Srimanote, P

2013-11-01

Isolates of Streptococcus suis from different Western countries as well as those from China and Vietnam have been previously well characterized. So far, the genetic characteristics and relationship between S. suis strains isolated from both humans and pigs in Thailand are unknown. In this study, a total of 245 S. suis isolates were collected from both human cases (epidemic and sporadic) and pigs (diseased and asymptomatic) in Thailand. Bacterial strains were identified by biochemical tests and PCR targeting both, the 16S rRNA and gdh genes. Thirty-six isolates were identified as serotype 2 based on serotyping and the cps2-PCR. These isolates were tested for the presence of six virulence-associated genes: an arginine deiminase (arcA), a 38-kDa protein and protective antigen (bay046), an extracellular factor (epf), an hyaluronidase (hyl), a muramidase-released protein (mrp) and a suilysin (sly). In addition, the genetic diversities of these isolates were studied by RAPD PCR and multilocus sequence typing (MLST) analysis. Four virulence-associated gene patterns (VAGP 1 to 4) were obtained, and the majority of isolates (32/36) carried all genes tested (VAGP1). Each of the three OPB primers used provided 4 patterns designated RAPD-A to RAPD-D. Furthermore, MLST analysis could also distinguish the 36 isolates into four sequence types (STs): ST1 (n = 32), ST104 (n = 2), ST233 (n = 1) and a newly identified ST, ST336 (n = 1). Dendrogram constructions based on RAPD patterns indicated that S. suis serotype 2 isolates from Thailand could be divided into four groups and that the characteristics of the individual groups were in complete agreement with the virulence gene profiles and STs. The majority (32/36) of isolates recovered from diseased pigs, slaughterhouse pigs or human patients could be classified into a single group (VAGP1, RAPD-A and ST1). This genetic information strongly suggests the transmission of S. suis isolates from pigs to humans in Thailand. Our findings are

Comparison of the Diversity of Basidiomycetes from Dead Wood of the Manchurian fir (Abies holophylla) as Evaluated by Fruiting Body Collection, Mycelial Isolation, and 454 Sequencing.

Science.gov (United States)

Jang, Yeongseon; Jang, Seokyoon; Min, Mihee; Hong, Joo-Hyun; Lee, Hanbyul; Lee, Hwanhwi; Lim, Young Woon; Kim, Jae-Jin

2015-10-01

In this study, three different methods (fruiting body collection, mycelial isolation, and 454 sequencing) were implemented to determine the diversity of wood-inhabiting basidiomycetes from dead Manchurian fir (Abies holophylla). The three methods recovered similar species richness (26 species from fruiting bodies, 32 species from mycelia, and 32 species from 454 sequencing), but Fisher's alpha, Shannon-Wiener, Simpson's diversity indices of fungal communities indicated fruiting body collection and mycelial isolation displayed higher diversity compared with 454 sequencing. In total, 75 wood-inhabiting basidiomycetes were detected. The most frequently observed species were Heterobasidion orientale (fruiting body collection), Bjerkandera adusta (mycelial isolation), and Trichaptum fusco-violaceum (454 sequencing). Only two species, Hymenochaete yasudae and Hypochnicium karstenii, were detected by all three methods. This result indicated that Manchurian fir harbors a diverse basidiomycetous fungal community and for complete estimation of fungal diversity, multiple methods should be used. Further studies are required to understand their ecology in the context of forest ecosystems.

Isolation of diverse members of the Aquificales from geothermal springs in Tengchong, China

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Brian P. Hedlund

2015-02-01

Full Text Available The order Aquificales (phylum Aquificae consists of thermophilic and hyperthermophilic bacteria that are prominent in many geothermal systems, including those in Tengchong, Yunnan Province, China. However, Aquificales have not previously been isolated from Tengchong. We isolated five strains of Aquificales from diverse springs (temperature 60.0-82.9°C and pH 2.6-8.9 in the Rehai Geothermal Field from sites in which Aquificales were abundant. Phylogenetic analysis showed that four of the strains belong to the genera Hydrogenobacter, Hydrogenobaculum, and Sulfurihydrogenibium, including strains distant enough to likely justify new species of Hydrogenobacter and Hydrogenobaculum. The additional strain may represent a new genus in the Hydrogenothermaceae. All strains were capable of aerobic respiration under microaerophilic conditions; however, they had variable capacity for chemolithotrophic oxidation of hydrogen and sulfur compounds and nitrate reduction.

Diverse urban plantings managed with sufficient resource availability can increase plant productivity and arthropod diversity

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Jonathon eMuller

2014-10-01

Full Text Available Buildings structures and surfaces are explicitly being used to grow plants, and these ‘urban plantings’ are typically designed for aesthetic value. Urban plantings also have the potential to contribute significant ‘ecological values’ by increasing urban habitat for animals such as arthropods and by increasing plant productivity. In this study, we evaluated how the provision of these additional ecological values is affected by plant species richness; the availability of essential resources for plants, such as water, light, space; and soil characteristics. We sampled 33 plantings located on the exterior of three buildings in the urban centre of Brisbane, Australia (subtropical climatic region over two, six week sampling periods characterised by different temperature and rainfall conditions. Plant cover was estimated as a surrogate for productivity as destructive sampling of biomass was not possible. We measured weekly light levels (photosynthetically active radiation, plant CO2 assimilation, soil CO2 efflux, and arthropod diversity.Differences in plant cover were best explained by a three-way interaction of plant species richness, management water regime and sampling period. As the richness of plant species increased in a planter, productivity and total arthropod richness also increased significantly - likely due to greater habitat heterogeneity and quality. Overall we found urban plantings can provide additional ecological values if essential resources are maintained within a planter such as water, light and soil temperature. Diverse urban plantings that are managed with these principles in mind can contribute to the attraction of diverse arthropod communities, and lead to increased plant productivity within a dense urban context.

Immigration Ethnic Diversity and Political Outcomes

DEFF Research Database (Denmark)

Harmon, Nikolaj Arpe

2017-01-01

I study the impact of immigration and increasing ethnic diversity on political outcomes in immigrant-receiving countries, focusing on immigration and election outcomes in Danish municipalities 1981-2001. A rich set of control variables isolates ethnic diversity effects from those of other immigrant...... characteristics and a novel IV strategy based on historical housing stock data addresses issues of endogenous location choices of immigrants. Increases in local ethnic diversity lead to right-ward shifts in election outcomes by shifting electoral support away from traditional "big government" left-wing parties...... and towards anti-immigrant nationalist parties in particular. These effects appear in both local and national elections....

The genetic diversity and phenotypic characterisation of Streptococcus agalactiae isolates from Rio de Janeiro, Brazil

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Ana Beatriz de Almeida Corrêa

2011-12-01

Full Text Available Streptococcus agalactiae isolates are more common among pregnant women, neonates and nonpregnant adults with underlying diseases compared to other demographic groups. In this study, we evaluate the genetic and phenotypic diversity in S. agalactiae strains from Rio de Janeiro (RJ that were isolated from asymptomatic carriers. We analysed these S. agalactiae strains using pulsed-field gel electrophoresis (PFGE, serotyping and antimicrobial susceptibility testing, as well as by determining the macrolide resistance phenotype, and detecting the presence of the ermA/B, mefA/E and lnuB genes. The serotypes Ia, II, III and V were the most prevalent serotypes observed. The 60 strains analysed were susceptible to penicillin, vancomycin and levofloxacin. Resistance to clindamycin, chloramphenicol, erythromycin, rifampin and tetracycline was observed. Among the erythromycin and/or clindamycin resistant strains, the ermA, ermB and mefA/E genes were detected and the constitutive macrolides, lincosamides and streptogramin B-type resistance was the most prevalent phenotype observed. The lnuB gene was not detected in any of the strains studied. We found 56 PFGE electrophoretic profiles and only 22 of them were allocated in polymorphism patterns. This work presents data on the genetic diversity and prevalent capsular serotypes among RJ isolates. Approximately 85% of these strains came from pregnant women; therefore, these data may be helpful in developing future prophylaxis and treatment strategies for neonatal syndromes in RJ.

As Clear as Mud? Determining the Diversity and Prevalence of Prophages in the Draft Genomes of Estuarine Isolates of Clostridium difficile.

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Hargreaves, Katherine R; Otieno, James R; Thanki, Anisha; Blades, Matthew J; Millard, Andrew D; Browne, Hilary P; Lawley, Trevor D; Clokie, Martha R J

2015-05-27

The bacterium Clostridium difficile is a significant cause of nosocomial infections worldwide. The pathogenic success of this organism can be attributed to its flexible genome which is characterized by the exchange of mobile genetic elements, and by ongoing genome evolution. Despite its pathogenic status, C. difficile can also be carried asymptomatically, and has been isolated from natural environments such as water and sediments where multiple strain types (ribotypes) are found in close proximity. These include ribotypes which are associated with disease, as well as those that are less commonly isolated from patients. Little is known about the genomic content of strains in such reservoirs in the natural environment. In this study, draft genomes have been generated for 13 C. difficile isolates from estuarine sediments including clinically relevant and environmental associated types. To identify the genetic diversity within this strain collection, whole-genome comparisons were performed using the assemblies. The strains are highly genetically diverse with regards to the C. difficile "mobilome," which includes transposons and prophage elements. We identified a novel transposon-like element in two R078 isolates. Multiple, related and unrelated, prophages were detected in isolates across ribotype groups, including two novel prophage elements and those related to the transducing phage φC2. The susceptibility of these isolates to lytic phage infection was tested using a panel of characterized phages found from the same locality. In conclusion, estuarine sediments are a source of genetically diverse C. difficile strains with a complex network of prophages, which could contribute to the emergence of new strains in clinics. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes

Science.gov (United States)

Bruskiewich, Richard; Burris, Jason N.; Carrigan, Charlotte T.; Chase, Mark W.; Clarke, Neil D.; Covshoff, Sarah; dePamphilis, Claude W.; Edger, Patrick P.; Goh, Falicia; Graham, Sean; Greiner, Stephan; Hibberd, Julian M.; Jordon-Thaden, Ingrid; Kutchan, Toni M.; Leebens-Mack, James; Melkonian, Michael; Miles, Nicholas; Myburg, Henrietta; Patterson, Jordan; Pires, J. Chris; Ralph, Paula; Rolf, Megan; Sage, Rowan F.; Soltis, Douglas; Soltis, Pamela; Stevenson, Dennis; Stewart, C. Neal; Surek, Barbara; Thomsen, Christina J. M.; Villarreal, Juan Carlos; Wu, Xiaolei; Zhang, Yong; Deyholos, Michael K.; Wong, Gane Ka-Shu

2012-01-01

Next-generation sequencing plays a central role in the characterization and quantification of transcriptomes. Although numerous metrics are purported to quantify the quality of RNA, there have been no large-scale empirical evaluations of the major determinants of sequencing success. We used a combination of existing and newly developed methods to isolate total RNA from 1115 samples from 695 plant species in 324 families, which represents >900 million years of phylogenetic diversity from green algae through flowering plants, including many plants of economic importance. We then sequenced 629 of these samples on Illumina GAIIx and HiSeq platforms and performed a large comparative analysis to identify predictors of RNA quality and the diversity of putative genes (scaffolds) expressed within samples. Tissue types (e.g., leaf vs. flower) varied in RNA quality, sequencing depth and the number of scaffolds. Tissue age also influenced RNA quality but not the number of scaffolds ≥1000 bp. Overall, 36% of the variation in the number of scaffolds was explained by metrics of RNA integrity (RIN score), RNA purity (OD 260/230), sequencing platform (GAIIx vs HiSeq) and the amount of total RNA used for sequencing. However, our results show that the most commonly used measures of RNA quality (e.g., RIN) are weak predictors of the number of scaffolds because Illumina sequencing is robust to variation in RNA quality. These results provide novel insight into the methods that are most important in isolating high quality RNA for sequencing and assembling plant transcriptomes. The methods and recommendations provided here could increase the efficiency and decrease the cost of RNA sequencing for individual labs and genome centers. PMID:23185583

Intraclonal genome diversity of Pseudomonas aeruginosa clones CHA and TB

Science.gov (United States)

2013-01-01

Background Adaptation of Pseudomonas aeruginosa to different living conditions is accompanied by microevolution resulting in genomic diversity between strains of the same clonal lineage. In order to detect the impact of colonized habitats on P. aeruginosa microevolution we determined the genomic diversity between the highly virulent cystic fibrosis (CF) isolate CHA and two temporally and geographically unrelated clonal variants. The outcome was compared with the intraclonal genome diversity between three more closely related isolates of another clonal complex. Results The three clone CHA isolates differed in their core genome in several dozen strain specific nucleotide exchanges and small deletions from each other. Loss of function mutations and non-conservative amino acid replacements affected several habitat- and lifestyle-associated traits, for example, the key regulator GacS of the switch between acute and chronic disease phenotypes was disrupted in strain CHA. Intraclonal genome diversity manifested in an individual composition of the respective accessory genome whereby the highest number of accessory DNA elements was observed for isolate PT22 from a polluted aquatic habitat. Little intraclonal diversity was observed between three spatiotemporally related outbreak isolates of clone TB. Although phenotypically different, only a few individual SNPs and deletions were detected in the clone TB isolates. Their accessory genome mainly differed in prophage-like DNA elements taken up by one of the strains. Conclusions The higher geographical and temporal distance of the clone CHA isolates was associated with an increased intraclonal genome diversity compared to the more closely related clone TB isolates derived from a common source demonstrating the impact of habitat adaptation on the microevolution of P. aeruginosa. However, even short-term habitat differentiation can cause major phenotypic diversification driven by single genomic variation events and uptake of phage

Genetic diversity of Clavispora lusitaniae isolated from Agave fourcroydes Lem, as revealed by DNA fingerprinting.

Science.gov (United States)

Pérez-Brito, Daisy; Magaña-Alvarez, Anuar; Lappe-Oliveras, Patricia; Cortes-Velazquez, Alberto; Torres-Calzada, Claudia; Herrera-Suarez, Teófilo; Larqué-Saavedra, Alfonso; Tapia-Tussell, Raul

2015-01-01

This study characterized Clavispora lusitaniae strains isolated from different stages of the processing and early fermentation of a henequen (Agave fourcroydes) spirit produced in Yucatan, Mexico using a molecular technique. Sixteen strains identified based on morphological features, obtained from different substrates, were typed molecularly. Nine different versions of the divergent D1/D2 domain of the large-subunit ribosomal DNA sequence were identified among the C. lusitaniae strains. The greatest degree of polymorphism was found in the 90-bp structural motif of the D2 domain. The MSP-PCR technique was able to differentiate 100% of the isolates. This study provides significant insight into the genetic diversity of the mycobiota present during the henequen fermentation process, especially that of C. lusitaniae, for which only a few studies in plants have been published. The applied MSP-PCR markers were very efficient in revealing olymorphisms between isolates of this species.

Is surgical workforce diversity increasing?

Science.gov (United States)

Andriole, Dorothy A; Jeffe, Donna B; Schechtman, Kenneth B

2007-03-01

We sought to determine the extent to which recent increases in levels of gender and racial diversity in the overall resident-physician workforce were evident among core-surgical specialty resident workforces. Chi-square tests for trend assessed the importance of changes from 1996 to 2004 in proportions of women and African Americans in the surgery-resident workforce. Surgery-resident trends were compared with overall resident workforce trends using two-tailed t-tests to compare regression slopes that quantified rates of change over time. Chi-square tests assessed differences between proportions of women and African Americans in the current overall board-certified workforce and their proportions in the surgery board-certified workforce. From 1996 to 2004, proportions of women increased in all seven surgical specialties studied. Compared with the overall trend toward increasing proportions of women in the resident workforce, the trend in one surgical specialty was larger (obstetrics/gynecology, p 0.05), and two were smaller (each p 0.05). Proportions of African Americans decreased in three specialties (each p workforce, except obstetrics/gynecology, remained lower than in the overall board-certified workforce (each p workforces have persisted since 1996 and will likely perpetuate ongoing surgery board-certified workforce disparities.

Social Isolation and Social Cohesion: The Effects of K-12 Neighborhood and School Segregation on Intergroup Orientations

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Braddock, Jomills Henry, II; Gonzalez, Amaryllis Del Carmen

2010-01-01

Background/Context: The United States is becoming increasingly racially and ethnically diverse, and increasingly racially isolated across race-ethnic boundaries. Researchers have argued that both diversity and racial isolation serve to undermine the social cohesion needed to bind American citizens to one another and to society at large. Focus of…

Diversity of Saccharomyces cerevisiae strains isolated from Borassus akeassii palm wines from Burkina Faso in comparison to other African beverages.

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Tapsoba, François; Legras, Jean-Luc; Savadogo, Aly; Dequin, Sylvie; Traore, Alfred Sababenedyo

2015-10-15

In South-West of Burkina Faso, palm wine is produced by spontaneous fermentation of the sap from a specific palm tree Borassus akeassii and plays an important role in people's lives. Saccharomyces cerevisiae is the main agent of this alcoholic fermentation but little is known about the diversity of the isolates from palm. In this work, 39 Saccharomyces cerevisiae strains were isolated from palm wine samples collected from 14 sites in Burkina Faso, as well as 7 isolates obtained from sorghum beer (Dolo) from 3 distant sites. Their diversity was analyzed at 12 microsatellite loci, and compared to the genotypes obtained for other African yeast populations isolated from Cocoa hulks from Ghana, sorghum beer from Ivory Coast, palm wine from Djibouti Republic, and to our database of strains from miscellaneous origins (bread, beer, wine, sake, oaks…). The ploidy of these strains has been assessed as well by flow cytometry. Our results show that B. akeassii palm wine contains a specific yeast population of diploid strains, different from Dolo produced in the same area and from other palm wine strains from Ivory Coast, Nigeria, or Djibouti Republic. In contrast, Dolo strains appeared as a group of related and mainly tetraploid strains despite being isolated from different countries. Copyright © 2015 Elsevier B.V. All rights reserved.

Increasing crop diversity mitigates weather variations and improves yield stability.

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Gaudin, Amélie C M; Tolhurst, Tor N; Ker, Alan P; Janovicek, Ken; Tortora, Cristina; Martin, Ralph C; Deen, William

2015-01-01

Cropping sequence diversification provides a systems approach to reduce yield variations and improve resilience to multiple environmental stresses. Yield advantages of more diverse crop rotations and their synergistic effects with reduced tillage are well documented, but few studies have quantified the impact of these management practices on yields and their stability when soil moisture is limiting or in excess. Using yield and weather data obtained from a 31-year long term rotation and tillage trial in Ontario, we tested whether crop rotation diversity is associated with greater yield stability when abnormal weather conditions occur. We used parametric and non-parametric approaches to quantify the impact of rotation diversity (monocrop, 2-crops, 3-crops without or with one or two legume cover crops) and tillage (conventional or reduced tillage) on yield probabilities and the benefits of crop diversity under different soil moisture and temperature scenarios. Although the magnitude of rotation benefits varied with crops, weather patterns and tillage, yield stability significantly increased when corn and soybean were integrated into more diverse rotations. Introducing small grains into short corn-soybean rotation was enough to provide substantial benefits on long-term soybean yields and their stability while the effects on corn were mostly associated with the temporal niche provided by small grains for underseeded red clover or alfalfa. Crop diversification strategies increased the probability of harnessing favorable growing conditions while decreasing the risk of crop failure. In hot and dry years, diversification of corn-soybean rotations and reduced tillage increased yield by 7% and 22% for corn and soybean respectively. Given the additional advantages associated with cropping system diversification, such a strategy provides a more comprehensive approach to lowering yield variability and improving the resilience of cropping systems to multiple environmental

Detecting the Diversity of Mycoplasma and Ureaplasma Endosymbionts Hosted by Trichomonas vaginalis Isolates

Science.gov (United States)

Ioannidis, Anastasios; Papaioannou, Panagiota; Magiorkinis, Emmanouil; Magana, Maria; Ioannidou, Vasiliki; Tzanetou, Konstantina; Burriel, Angeliki R.; Tsironi, Maria; Chatzipanagiotou, Stylianos

2017-01-01

Objectives: The symbiosis of Trichomonas vaginalis and Mycoplasma hominis is the first described association between two obligate human parasites. Trichomonas is the niche and the vector for the transmission of M. hominis infection. This clinically significant symbiosis may affect T. vaginalis virulence and susceptibility to treatment. The aims of this study were to investigate the intracellularly present Mycoplasma and Ureaplasma species in T. vaginalis strains isolated from the vaginal discharge of infected women as well as to trace the diversity pattern among the species detected in the isolated strains. Methods: Hundred pure T. vaginalis cultures were isolated from ~7,500 patient specimens presented with clinical purulent vaginitis. PCR and sequencing for Mycoplasma/Ureaplasma spp. were performed in DNA extracted from the pure cultures. In addition, vaginal discharge samples were cultured for the presence of M. hominis and U. urealyticum. Phylogenetic analysis assisted the identification of interspecies relationships between the Mycoplasma and Ureaplasma isolates. Results: Fifty four percentage of T. vaginalis isolates were harboring Mycoplasma spp. Phylogenetic analysis revealed three distinct clusters, two with already characterized M. hominis and Ureaplasma spp. (37% of total Mycoplasma spp.), whereas one group formed a distinct cluster matched with the newly identified species Candidatus Mycoplasma girerdii (59.3%) and one or more unknown Mycoplasma spp. (3.7%). Conclusions: T. vaginalis strains associated with vaginal infection might host intracellular mycoplasmas or ureaplasmas. Intracellular Mollicutes that remain undetected in the extracellular environment when conventional diagnostic methods are implemented may comprise either novel species, such as Candidatus M. giredii, or unknown species with yet unexplored clinical significance. PMID:28702014

Detecting the Diversity of Mycoplasma and Ureaplasma Endosymbionts Hosted by Trichomonas vaginalis Isolates

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Anastasios Ioannidis

2017-06-01

Full Text Available Objectives: The symbiosis of Trichomonas vaginalis and Mycoplasma hominis is the first described association between two obligate human parasites. Trichomonas is the niche and the vector for the transmission of M. hominis infection. This clinically significant symbiosis may affect T. vaginalis virulence and susceptibility to treatment. The aims of this study were to investigate the intracellularly present Mycoplasma and Ureaplasma species in T. vaginalis strains isolated from the vaginal discharge of infected women as well as to trace the diversity pattern among the species detected in the isolated strains.Methods: Hundred pure T. vaginalis cultures were isolated from ~7,500 patient specimens presented with clinical purulent vaginitis. PCR and sequencing for Mycoplasma/Ureaplasma spp. were performed in DNA extracted from the pure cultures. In addition, vaginal discharge samples were cultured for the presence of M. hominis and U. urealyticum. Phylogenetic analysis assisted the identification of interspecies relationships between the Mycoplasma and Ureaplasma isolates.Results: Fifty four percentage of T. vaginalis isolates were harboring Mycoplasma spp. Phylogenetic analysis revealed three distinct clusters, two with already characterized M. hominis and Ureaplasma spp. (37% of total Mycoplasma spp., whereas one group formed a distinct cluster matched with the newly identified species Candidatus Mycoplasma girerdii (59.3% and one or more unknown Mycoplasma spp. (3.7%.Conclusions:T. vaginalis strains associated with vaginal infection might host intracellular mycoplasmas or ureaplasmas. Intracellular Mollicutes that remain undetected in the extracellular environment when conventional diagnostic methods are implemented may comprise either novel species, such as Candidatus M. giredii, or unknown species with yet unexplored clinical significance.

Diversity patterns and isolation of Planctomycetes associated with metalliferous deposits from hydrothermal vent fields along the Valu Fa Ridge (SW Pacific).

Science.gov (United States)

Storesund, Julia Endresen; Lanzèn, Anders; García-Moyano, Antonio; Reysenbach, Anna-Louise; Øvreås, Lise

2018-02-08

The microbial diversity associated with diffuse venting deep-sea hydrothermal deposits is tightly coupled to the geochemistry of the hydrothermal fluids. Previous 16S rRNA gene amplicon sequencing (metabarcoding) of marine iron-hydroxide deposits along the Arctic Mid Ocean Ridge, revealed the presence of diverse bacterial communities associated with these deposits (Storesund and Øvreås in Antonie van Leeuwenhoek 104:569-584, 2013). One of the most abundant and diverse phyla detected was the enigmatic Planctomycetes. Here we report on the comparative analyses of the diversity and distribution patterns of Planctomycetes associated with metalliferous deposits from two diffuse-flow hydrothermal vent fields (Mariner and Vai Lili) from the Valu Fa Ridge in the Southwestern Pacific. Metabarcoding of 16S rRNA genes showed that the major prokaryotic phyla were Proteobacteria (51-73% of all 16S rRNA gene reads), Epsilonbacteraeota (0.5-19%), Bacteriodetes (5-17%), Planctomycetes (0.4-11%), Candidatus Latescibacteria (0-5%) and Marine Benthic Group E (Hydrothermarchaeota) (0-5%). The two different sampling sites differed considerably in overall community composition. The abundance of Planctomycetes also varied substantially between the samples and the sites, with the majority of the sequences affiliated with uncultivated members of the classes Planctomycetacia and Phycisphaerae, and other deep branching lineages. Seven different strains affiliated with the order Planctomycetales were isolated, mostly from the Vai Lili samples, where also the highest Planctomycetales diversity was seen. Most of the isolates were affiliated with the genera Gimesia, Rhodopirellula and Blastopirellula. One isolate was only distantly related to known cultured, but uncharacterized species within the Pir4 group. This study shows that the deep-sea Planctomycetes represent a very heterogeneous group with a high phylogenetic diversity and a substantial potential for novel organism discovery in these

Increasing Diversity in K-12 School Leadership. Policy Brief 2018-3

Science.gov (United States)

Castro, Andrene; Germain, Emily; Gooden, Mark

2018-01-01

Principals represent the most "visible" form of leadership in schools, but current workforce data show that K-12 school principals are overwhelmingly white and fail to reflect the diversity within the student population. With increased policy focus on teacher diversity, equal attention must also be directed towards the lack of diversity…

Progesterone pretreatment increases the stress response to social isolation in ewes.

Science.gov (United States)

Freitas-de-Melo, Aline; Damián, Juan Pablo; Hötzel, Maria José; Banchero, Georgget; Ungerfeld, Rodolfo

2016-01-01

In rodents, progesterone (P4) pretreatment increases anxiety and response to stressors. Social isolation is a stressor that generates physiological and behavioural stress responses in sheep. The aim of the study was to compare the stress response of anoestrous ewes previously treated or not with P4 to the social isolation test. Ten ewes received P4 treatment during 13 d (group P4-W) and another 10 remained untreated as controls (group Con). The ewes were individually isolated in a novel place during 10 min, 24 h after the end of P4 pretreatment and their behaviours were recorded. Cortisol and P4 concentrations as well as body surface temperature were recorded before and after the test. Ewes of the P4-W group presented higher cortisol levels 0, 10, 20 and 30 min after the social isolation and had greater area under the curve of cortisol compared to Con ewes (41,785%±4,156% vs. 25,682%±4,565% during 75 min). Progesterone and body surface temperature increased after social isolation, with no differences between P4-W and Con ewes. There were no differences in behavioural responses to social isolation. P4 pretreatment appears to augment the stress response to social isolation in anoestrous ewes.

Genetic diversity of Plasmodium falciparum isolates from naturally infected children in north-central Nigeria using the merozoite surface protein-2 as molecular marker.

Science.gov (United States)

Oyedeji, Segun Isaac; Awobode, Henrietta Oluwatoyin; Anumudu, Chiaka; Kun, Jürgen

2013-08-01

To characterize the genetic diversity of Plasmodium falciparum (P. falciparum) field isolates in children from Lafia, North-central Nigeria, using the highly polymorphic P. falciparum merozoite surface protein 2 (MSP-2) gene as molecular marker. Three hundred and twenty children were enrolled into the study between 2005 and 2006. These included 140 children who presented with uncomplicated malaria at the Dalhatu Araf Specialist Hospital, Lafia and another 180 children from the study area with asymptomatic infection. DNA was extracted from blood spot on filter paper and MSP-2 genes were genotyped using allele-specific nested PCR in order to analyze the genetic diversity of parasite isolates. A total of 31 and 34 distinct MSP-2 alleles were identified in the asymptomatic and uncomplicated malaria groups respectively. No difference was found between the multiplicity of infection in the asymptomatic group and that of the uncomplicated malaria group (P>0.05). However, isolates of the FC27 allele type were dominant in the asymptomatic group whereas isolates of the 3D7 allele type were dominant in the uncomplicated malaria group. This study showed a high genetic diversity of P. falciparum isolates in North-central Nigeria and is comparable to reports from similar areas with high malaria transmission intensity. Copyright © 2013 Hainan Medical College. Published by Elsevier B.V. All rights reserved.

An investigation of the subtype diversity of clinical isolates of Irish Clostridium difficile ribotypes 027 and 078 by repetitive-extragenic palindromic PCR.

LENUS (Irish Health Repository)

Solomon, K

2011-08-01

A repetitive-extragenic palindromic PCR (rep-PCR) subtyping method (DiversiLab) in conjunction with ribotyping, toxinotyping and antimicrobial-susceptibility testing was used to detect subtypes within Clostridium difficile ribotypes 027 and 078. Clinical isolates of ribotypes 027 (toxinotype III) (n = 30) and 078 (toxinotype V) (n = 23) were provided by health-care facilities across the Republic of Ireland over 2 months in 2006 and 1 month in 2009. Ribotype 027 isolates were significantly more related to each other (9 different subtype profiles) when compared to ribotype 078 isolates (14 different profiles) (P = 0.001; cut-off >90 % similarity). Almost half of ribotype 078 isolates (45.5 %) showed no relationship to each other. The clonality of ribotype 027 isolates suggests effective adaptation to the human niche, whereas the considerable genetic diversity within ribotype 078 isolates suggests that they may have originated from a variety of sources. Subtyping correlated well with antimicrobial susceptibility, in particular clindamycin susceptibility for ribotype 027, but diverse antimicrobial-susceptibility profiles were seen in ribotype 078 isolates, even within a single health-care facility. Between 2006 and 2009, a change in the predominant subtype of ribotype 027 was seen, with the recent clone representing half of all ribotype 027 isolates studied. This strain exhibited 89 % similarity to a rep-PCR profile of the North American NAP-1 strain.

Diversity and phosphate solubilization by bacteria isolated from Laki Island coastal ecosystem

Directory of Open Access Journals (Sweden)

SRI WIDAWATI

2011-01-01

Full Text Available Widawati S (2011 Diversity and phosphate solubilization by bacteria isolated from Laki Island coastal ecosystem. Biodiversitas 12: 17-21. Soil, water, sand, and plant rhizosphere samples collected from coastal ecosystem of Laki Island-Jakarta were screened for phosphate solubilizing bacteria (PSB. While the population was dependent on the cultivation media and the sample type, the highest bacterial population was observed in the rhizosphere of Ipomea aquatica. The PSB strains isolated from the sample registered 18.59 g-1L-1, 18.31 g-1L-1, and 5.68 g-1L-1 of calcium phosphate (Ca-P, Al-P and rock phosphate solubilization after 7-days. Phosphate solubilizing capacity was the highest in the Ca-P medium. Two strains, 13 and 14, registered highest Phosphomonoesterase activities (2.01 µgNP.g-1.h-1 and 1.85NP µg.g-1.h-1 were identified as Serattia marcescens, and Pseudomonas fluorescense, respectively. Both strains were isolated from the crops of Amaranthus hybridus and I. aquatica, respectively, which are commonly observed in coastal ecosystems. The presence of phosphate solubilizing microorganisms and their ability to solubilize various types of phosphate species are indicative of the important role of both species of bacteria in the biogeochemical cycle of phosphorus and the plant growth in coastal ecosystems.

Genetic diversity of Mycoplasma hyopneumoniae isolates of abattoir pigs.

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Charlebois, Audrey; Marois-Créhan, Corinne; Hélie, Pierre; Gagnon, Carl A; Gottschalk, Marcelo; Archambault, Marie

2014-01-31

Mycoplasma hyopneumoniae, the causative agent of porcine enzootic pneumonia, is present in swine herds worldwide. However, there is little information on strains infecting herds in Canada. A total of 160 swine lungs with lesions suggestive of enzootic pneumonia originating from 48 different farms were recovered from two slaughterhouses and submitted for gross pathology. The pneumonic lesion scores ranged from 2% to 84%. Eighty nine percent of the lungs (143/160) were positive for M. hyopneumoniae by real-time PCR whereas 10% (16/160) and 8.8% (14/160) were positive by PCR for M. hyorhinis and M. flocculare, respectively. By culture, only 6% of the samples were positive for M. hyopneumoniae (10/160). Among the selected M. hyopneumoniae-positive lungs (n=25), 9 lungs were co-infected with M. hyorhinis, 9 lungs with PCV2, 2 lungs with PRRSV, 12 lungs with S. suis and 10 lungs with P. multocida. MLVA and PCR-RFLP clustering of M. hyopneumoniae revealed that analyzed strains were distributed among three and five clusters respectively, regardless of severity of lesions, indicating that no cluster is associated with virulence. However, strains missing a specific MLVA locus showed significantly less severe lesions and lower numbers of bacteria. MLVA and PCR-RFLP analyses also showed a high diversity among field isolates of M. hyopneumoniae with a greater homogeneity within the same herd. Almost half of the field isolates presented less than 55% homology with selected vaccine and reference strains. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Patterns of bird functional diversity on land-bridge island fragments.

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Ding, Zhifeng; Feeley, Kenneth J; Wang, Yanping; Pakeman, Robin J; Ding, Ping

2013-07-01

The loss of species diversity due to habitat fragmentation has been extensively studied. In contrast, the impacts of habitat fragmentation on functional diversity remains relatively poorly understood. We conducted bird functional diversity studies on a set of 41 recently isolated land-bridge islands in the Thousand Island Lake, China. We analysed differences in bird species richness and a recently developed suite of complementary functional diversity indices (FRic, volume of functional space occupied; FEve, evenness of abundance distribution in the functional trait space; FDiv, divergence in the distribution of abundance in the trait volume) across different gradients (island area and isolation). We found no correlations between FRic and FEve or FEve and FDiv, but negative correlations between FRic and FDiv. As predicted, island area accounted for most of the variation in bird species richness, whereas isolation explained most of the variation in species evenness (decreasing species evenness with increasing isolation). Functional diversity appears to be more strongly influenced by habitat filtering as opposed to limiting similarity. More specifically, across all islands, both FRic and FEve were significantly lower than expected for randomly assembled communities, but FDiv showed no clear patterns. FRic increased with island area, FEve decreased with island area and FDiv showed no clear patterns. Our finding that FEve decreases with island area at TIL may indicate low functional stability on such islands, and as such large islands and habitat patches may deserve extra attention and/or protection. These results help to demonstrate the importance of considering the effects of fragmentation on functional diversity in habitat management and reserve design plans. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

Low-Level Exploitation Mitigation by Diverse Microservices

OpenAIRE

Otterstad , Christian; Yarygina , Tetiana

2017-01-01

Part 2: Microservices and Containers; International audience; This paper discusses a combination of isolatable microservices and software diversity as a mitigation technique against low-level exploitation; the effectiveness and benefits of such an architecture are substantiated. We argue that the core security benefit of microservices with diversity is increased control flow isolation. Additionally, a new microservices mitigation technique leveraging a security monitor service is introduced t...

First insight into the genotypic diversity of clinical Mycobacterium tuberculosis isolates from Gansu Province, China.

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Jie Liu

Full Text Available BACKGROUND: Investigations of Mycobacterium tuberculosis genetic diversity in China have indicated a significant regional distribution. The aim of this study was to characterize the genotypes of clinical M. tuberculosis isolates obtained from Gansu, which has a special geographic location in China. METHODOLOGY/PRINCIPAL FINDINGS: A total of 467 clinical M. tuberculosis strains isolated in Gansu Province were genotyped by 15-locus mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR and spoligotyping. The results showed that 445 isolates belonged to six known spoligotype lineages, whereas 22 isolates were unknown. The Beijing genotype was the most prevalent (87.58%, n = 409, while the shared type 1 was the dominant genotype (80.94%, n = 378. The second most common lineage was the T lineage, with 25 isolates (5.35%, followed by the H lineage with 5 isolates (1.07%, the MANU family (0.64%, 3 isolates, the U family (0.43%, 2 isolates and the CAS lineage with 1 isolate (0.21%. By using the VNTR15China method, we observed 15 groups and 228 genotypes among the 467 isolates. We found no association between the five larger groups (including the Beijing genotype and sex, age, or treatment status, and there was no noticeable difference in the group analysis in different areas. In the present study, seven of the 15 MIRU-VNTR loci were highly or moderately discriminative according to their Hunter-Gaston discriminatory index. CONCLUSIONS/SIGNIFICANCE: The Beijing genotype is the predominant genotype in Gansu province. We confirm that VNTR15China is suitable for typing Beijing strains in China and that it has a better discriminatory power than spoligotyping. Therefore, the use of both methods is the most suitable for genotyping analysis of M. tuberculosis.

Diversity of lactic acid bacteria on organic flours and application of isolates in sourdough fermentation

OpenAIRE

Stanzer, Damir; Ivanuša, Ines; Kazazić, Snježana; Hanousek Čiča, Karla; Mrvčić, Jasna

2017-01-01

Organic farming preserves biodiversity and organic products can be the source of many microbial species. The species diversity in organically grown wheat, spelt and rye was investigated in order to find strains suitable for sourdough fermentation. Colonies representing various morphological appearances were isolated and catalase-negative colonies were identified by mass spectrometer Microflex LT ™ MALDI-TOF. The fermentation products (lactic, acetic, formic and phenyllactic acid) were determi...

Diversity and antimicrobial susceptibility of Salmonella enterica serovars isolated from pig farms in Ibadan, Nigeria

DEFF Research Database (Denmark)

Fashae, Kayode; Hendriksen, Rene S.

2014-01-01

of plasmid-mediated quinolone resistance (PMQR) genes in pigs in Ibadan, Nigeria. Pooled fresh pen floor fecal samples of pigs collected from 31 pig farms were cultured; the Salmonella isolates were serotyped and their antimicrobial susceptibility was determined. PMQR genes were screened by polymerase chain...... Kingston (n = 13; 5.7 %). The most widely distributed serovars among the farms were Salmonella Give (six farms) and Salmonella Elisaberthville (six farms). Resistance to chloramphenicol, sulfonamides, nalidixic acid, streptomycin, and tetracycline ranged from 11.6 % (n = 26) to 22.8 % (n = 51). Resistance....... Other PMQR genes were not detected. Pigs constitute an important source of diverse Salmonella serovars in Ibadan. The isolates were more resistant to old antimicrobials with some multiple resistant. Control measures and regulation of antimicrobials are warranted....

Molecular diversity of Mycobacterium tuberculosis isolates from patients with tuberculosis in Honduras

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Ghebremichael Solomon

2010-08-01

Full Text Available Abstract Background Tuberculosis persists as a public health problem in Honduras. A better knowledge of the molecular characteristics of Mycobacterium tuberculosis strains will contribute to understand the transmission dynamics of the disease within the country. The aim of this study was to provide an insight of the genetic biodiversity of M. tuberculosis clinical isolates collected in Honduras between 1994 and 2002. Genotyping was performed using spoligotyping and RFLP. The spoligotypes obtained were compared with the SITVIT2 proprietary database of the Pasteur Institute of Guadeloupe. Results Spoligotyping grouped 84% of the isolates into 27 clusters (2 to 43 strains per cluster. Of the 44 shared international types (SITs identified among the Honduran stains, 8 SITs were newly identified either within the present study or after match with an orphan type previously identified in the SITVIT2 database. In addition, 16 patterns corresponded to orphan, previously unreported isolates. The Latin American Mediterranean (LAM lineage was the most common in this study; 55% of the strains belonged to this family. Other genotypes found were Haarlem (16%, T (16%, X-clade (6%, Unknown signature (5% and S (1%. Only one Beijing strain was identified (0.5%. We observed a high degree of diversity after characterizing the 43 isolates belonging to the main spoligotyping cluster (SIT 33, LAM3 with IS6110-RFLP. A total of 35 different RFLP-fingerprints were detected, of which 6 patterns corresponded to the same number of clusters comprising 14 strains. Conclusions The findings obtained in this study show that tuberculosis transmission in Honduras is due to modern M. tuberculosis lineages with high level of biodiversity.

Molecular diversity of Mycobacterium tuberculosis isolates from patients with tuberculosis in Honduras

Science.gov (United States)

2010-01-01

Background Tuberculosis persists as a public health problem in Honduras. A better knowledge of the molecular characteristics of Mycobacterium tuberculosis strains will contribute to understand the transmission dynamics of the disease within the country. The aim of this study was to provide an insight of the genetic biodiversity of M. tuberculosis clinical isolates collected in Honduras between 1994 and 2002. Genotyping was performed using spoligotyping and RFLP. The spoligotypes obtained were compared with the SITVIT2 proprietary database of the Pasteur Institute of Guadeloupe. Results Spoligotyping grouped 84% of the isolates into 27 clusters (2 to 43 strains per cluster). Of the 44 shared international types (SITs) identified among the Honduran stains, 8 SITs were newly identified either within the present study or after match with an orphan type previously identified in the SITVIT2 database. In addition, 16 patterns corresponded to orphan, previously unreported isolates. The Latin American Mediterranean (LAM) lineage was the most common in this study; 55% of the strains belonged to this family. Other genotypes found were Haarlem (16%), T (16%), X-clade (6%), Unknown signature (5%) and S (1%). Only one Beijing strain was identified (0.5%). We observed a high degree of diversity after characterizing the 43 isolates belonging to the main spoligotyping cluster (SIT 33, LAM3) with IS6110-RFLP. A total of 35 different RFLP-fingerprints were detected, of which 6 patterns corresponded to the same number of clusters comprising 14 strains. Conclusions The findings obtained in this study show that tuberculosis transmission in Honduras is due to modern M. tuberculosis lineages with high level of biodiversity. PMID:20678242

Diversity and Antimicrobial Resistance Genotypes in Non-Typhoidal Salmonella Isolates from Poultry Farms in Uganda

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Terence Odoch

2018-02-01

Full Text Available Non-typhoidal Salmonella (NTS are foodborne pathogens of global public health significance. The aim of this study was to subtype a collection of 85 NTS originating from poultry farms in Uganda, and to evaluate a subgroup of phenotypically resistant isolates for common antimicrobial resistance genes and associated integrons. All isolates were subtyped by pulsed-field gel electrophoresis (PFGE. Phenotypically resistant isolates (n = 54 were screened by PCR for the most relevant AMR genes corresponding to their phenotypic resistance pattern, and all 54 isolates were screened by PCR for the presence of integron class 1 and 2 encoding genes. These genes are known to commonly encode resistance to ampicillin, tetracycline, ciprofloxacin, trimethoprim, sulfonamide and chloramphenicol. PFGE revealed 15 pulsotypes representing 11 serotypes from 75 isolates, as 10 were non-typable. Thirty one (57.4% of the 54 resistant isolates carried at least one of the seven genes (blaTEM-1, cmlA, tetA, qnrS, sul1, dhfrI, dhfrVII identified by PCR and six (11% carried class 1 integrons. This study has shown that a diversity of NTS-clones are present in Ugandan poultry farm settings, while at the same time similar NTS-clones occur in different farms and areas. The presence of resistance genes to important antimicrobials used in human and veterinary medicine has been demonstrated, hence the need to strengthen strategies to combat antimicrobial resistance at all levels.

Diversity of bacteria carried by pinewood nematode in USA and phylogenetic comparison with isolates from other countries.

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Diogo Neves Proença

Full Text Available Pine wilt disease (PWD is native to North America and has spread to Asia and Europe. Lately, mutualistic relationship has been suggested between the pinewood nematode (PWN, Bursaphelenchus xylophilus the causal nematode agent of PWD, and bacteria. In countries where PWN occurs, nematodes from diseased trees were reported to carry bacteria from several genera. However no data exists for the United States. The objective of this study was to evaluate the diversity of the bacterial community carried by B. xylophilus, isolated from different Pinus spp. with PWD in Nebraska, United States. The bacteria carried by PWN belonged to Gammaproteobacteria (79.9%, Betaproteobacteria (11.7%, Bacilli (5.0%, Alphaproteobacteria (1.7% and Flavobacteriia (1.7%. Strains from the genera Chryseobacterium and Pigmentiphaga were found associated with the nematode for the first time. These results were compared to results from similar studies conducted from other countries of three continents in order to assess the diversity of bacteria with associated with PWN. The isolates from the United States, Portugal and China belonged to 25 different genera and only strains from the genus Pseudomonas were found in nematodes from all countries. The strains from China were closely related to P. fluorescens and the strains isolated from Portugal and USA were phylogenetically related to P. mohnii and P. lutea. Nematodes from the different countries are associated with bacteria of different species, not supporting a relationship between PWN with a particular bacterial species. Moreover, the diversity of the bacteria carried by the pinewood nematode seems to be related to the geographic area and the Pinus species. The roles these bacteria play within the pine trees or when associated with the nematodes, might be independent of the presence of the nematode in the tree and only related on the bacteria's relationship with the tree.

Genetic diversity of Phytophthora sojae isolates in Heilongjiang Province in China assessed by RAPD and EST-SSR

Science.gov (United States)

Wu, J. J.; Xu, P. F.; Liu, L. J.; Wang, J. S.; Lin, W. G.; Zhang, S. Z.; Wei, L.

Random-amplified polymorphic DNA (RAPD) and EST-SSR markers were used to estimate the genetic relationship among thirty-nine P.sojae isolates from three locations in Heilongjiang Province, and nine isolates from Ohio in America were made as reference strains. 10 of 50 RAPD primers and 5 of 33 EST-SSR were polymorphic across 48 P.sojae isolates. Similarity values among P.sojae isolates were from 49% to 82% based on the RAPD data. The similarities based on EST-SSR markers ranged from 47% to 85%. The genetic diversity revealed by EST-SSR marker analysis was higher than that obtained from RAPD. The similarity matrices for the SSR data and the RAPD data were moderately correlated (r = 0.47). Genetic similarity coefficients were also relatively lower, which demonstrated complicated genetic background within each location. The high similarity values range revealed the ability of RAPD/EST-SSR markers to distinguish even among morphological similar phytophthora.

Genomic diversity of drug-resistant Mycobacterium tuberculosis isolates in Lisbon Portugal: Towards tuberculosis genomic epidemiology

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João Perdigão

2015-01-01

Full Text Available Multidrug- (MDR and extensively drug-resistant (XDR tuberculosis (TB present a challenge to disease control and elimination goals. Lisbon, Portugal, has a high TB incidencerate and unusual and successful XDR-TB strains that have been found in circulation foralmost two decades. For the last 20 years, a continued circulation of two phylogenetic clades, Lisboa3 and Q1, which are highly associated with MDR and XDR, have been observed. In recent years, these strains have been well characterized regarding the molecular basis of drug resistance and have been inclusively subjected to whole genome sequencing (WGS. Researchers have been studying the genomic diversity of strains circulating in Lisbon and its genomic determinants through cutting-edge next generation sequencing. An enormous amount of whole genome sequence data are now available for the most prevalent and clinically relevant strains circulating in Lisbon. It is the persistence, prevalence and rapid evolution towards drug resistance that has prompted researchers to investigate the properties of these strains at the genomic level and in the future at a global transcriptomic level. Seventy Mycobacterium tuberculosis (MTB isolates, mostly recovered in Lisbon, were genotyped by 24-loci Mycobacterial Interspersed Repetitive Unit – Variable Number of Tandem Repeats (MIRU-VNTR and the genomes sequenced using a next generation sequencing platform – Illumina HiSeq 2000. The genotyping data revealed three major clusters associated with MDR-TB (Lisboa3-A, Lisboa3-B and Q1, two of which are associated with XDR-TB (Lisboa3-B and Q1, whilst the genomic data contributed to elucidating the phylogenetic positioning of circulating MDR-TB strains, showing a high predominance of a single SNP cluster group 5. Furthermore, a genome-wide phylogeny analysis from these strains, together with 19 publicly available genomes of MTB clinical isolates, revealed two major clades responsible for MDR/XDR-TB in the region

Genomic diversity of drug-resistant Mycobacterium tuberculosis isolates in Lisbon Portugal: Towards tuberculosis genomic epidemiology

KAUST Repository

Perdigã o, Joã o; Silva, Hugo; Machado, Diana; Macedo, Rita; Maltez, Fernando; Silva, Carla; Jordao, Luisa; Couto, Isabel; Mallard, Kim; Coll, Francesc; Hill-Cawthorne, Grant A.; McNerney, Ruth; Pain, Arnab; Clark, Taane G.; Viveiros, Miguel; Portugal, Isabel

2015-01-01

Multidrug- (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) present a challenge to disease control and elimination goals. Lisbon, Portugal, has a high TB incidence rate and unusual and successful XDR-TB strains that have been found in circulation for almost two decades. For the last 20. years, a continued circulation of two phylogenetic clades, Lisboa3 and Q1, which are highly associated with MDR and XDR, have been observed. In recent years, these strains have been well characterized regarding the molecular basis of drug resistance and have been inclusively subjected to whole genome sequencing (WGS). Researchers have been studying the genomic diversity of strains circulating in Lisbon and its genomic determinants through cutting-edge next generation sequencing. An enormous amount of whole genome sequence data are now available for the most prevalent and clinically relevant strains circulating in Lisbon.It is the persistence, prevalence and rapid evolution towards drug resistance that has prompted researchers to investigate the properties of these strains at the genomic level and in the future at a global transcriptomic level. Seventy Mycobacterium tuberculosis (MTB) isolates, mostly recovered in Lisbon, were genotyped by 24-. loci Mycobacterial Interspersed Repetitive Unit - Variable Number of Tandem Repeats (MIRU-VNTR) and the genomes sequenced using a next generation sequencing platform - Illumina HiSeq 2000.The genotyping data revealed three major clusters associated with MDR-TB (Lisboa3-A, Lisboa3-B and Q1), two of which are associated with XDR-TB (Lisboa3-B and Q1), whilst the genomic data contributed to elucidating the phylogenetic positioning of circulating MDR-TB strains, showing a high predominance of a single SNP cluster group 5. Furthermore, a genome-wide phylogeny analysis from these strains, together with 19 publicly available genomes of MTB clinical isolates, revealed two major clades responsible for MDR/XDR-TB in the region: Lisboa3 and Q

Genomic diversity of drug-resistant Mycobacterium tuberculosis isolates in Lisbon Portugal: Towards tuberculosis genomic epidemiology

KAUST Repository

Perdigão, João

2015-03-01

Multidrug- (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) present a challenge to disease control and elimination goals. Lisbon, Portugal, has a high TB incidence rate and unusual and successful XDR-TB strains that have been found in circulation for almost two decades. For the last 20. years, a continued circulation of two phylogenetic clades, Lisboa3 and Q1, which are highly associated with MDR and XDR, have been observed. In recent years, these strains have been well characterized regarding the molecular basis of drug resistance and have been inclusively subjected to whole genome sequencing (WGS). Researchers have been studying the genomic diversity of strains circulating in Lisbon and its genomic determinants through cutting-edge next generation sequencing. An enormous amount of whole genome sequence data are now available for the most prevalent and clinically relevant strains circulating in Lisbon.It is the persistence, prevalence and rapid evolution towards drug resistance that has prompted researchers to investigate the properties of these strains at the genomic level and in the future at a global transcriptomic level. Seventy Mycobacterium tuberculosis (MTB) isolates, mostly recovered in Lisbon, were genotyped by 24-. loci Mycobacterial Interspersed Repetitive Unit - Variable Number of Tandem Repeats (MIRU-VNTR) and the genomes sequenced using a next generation sequencing platform - Illumina HiSeq 2000.The genotyping data revealed three major clusters associated with MDR-TB (Lisboa3-A, Lisboa3-B and Q1), two of which are associated with XDR-TB (Lisboa3-B and Q1), whilst the genomic data contributed to elucidating the phylogenetic positioning of circulating MDR-TB strains, showing a high predominance of a single SNP cluster group 5. Furthermore, a genome-wide phylogeny analysis from these strains, together with 19 publicly available genomes of MTB clinical isolates, revealed two major clades responsible for MDR/XDR-TB in the region: Lisboa3 and Q

Diversity structure of culturable bacteria isolated from the Fildes Peninsula (King George Island, Antarctica): A phylogenetic analysis perspective.

Science.gov (United States)

González-Rocha, Gerardo; Muñoz-Cartes, Gabriel; Canales-Aguirre, Cristian B; Lima, Celia A; Domínguez-Yévenes, Mariana; Bello-Toledo, Helia; Hernández, Cristián E

2017-01-01

It has been proposed that Antarctic environments select microorganisms with unique biochemical adaptations, based on the tenet 'Everything is everywhere, but, the environment selects' by Baas-Becking. However, this is a hypothesis that has not been extensively evaluated. This study evaluated the fundamental prediction contained in this hypothesis-in the sense that species are structured in the landscape according to their local habitats-, using as study model the phylogenetic diversity of the culturable bacteria of Fildes Peninsula (King George Island, Antarctica). Eighty bacterial strains isolated from 10 different locations in the area, were recovered. Based on phylogenetic analysis of 16S rRNA gene sequences, the isolates were grouped into twenty-six phylotypes distributed in three main clades, of which only six are exclusive to Antarctica. Results showed that phylotypes do not group significantly by habitat type; however, local habitat types had phylogenetic signal, which support the phylogenetic niche conservatism hypothesis and not a selective role of the environment like the Baas-Becking hypothesis suggests. We propose that, more than habitat selection resulting in new local adaptations and diversity, local historical colonization and species sorting (i.e. differences in speciation and extinction rates that arise by interaction of species level traits with the environment) play a fundamental role on the culturable bacterial diversity in Antarctica.

Bacterial isolates from the bryozoan Membranipora membranacea: influence of culture media on isolation and antimicrobial activity.

Science.gov (United States)

Heindl, Herwig; Thiel, Vera; Wiese, Jutta; Imhoff, Johannes F

2012-03-01

From specimens of the bryozoan Membranipora membranacea collected in the Baltic Sea, bacteria were isolated on four different media, which significantly increased the diversity of the isolated groups. All isolates were classified according to 16S rRNA gene sequence analysis and tested for antimicrobial properties using a panel of five indicator strains and six different media. Each medium featured a unique set of isolated phylotypes, and a phylogenetically diverse collection of isolates was obtained. A total of 96 isolates were assigned to 49 phylotypes and 29 genera. Only one-third of the members of these genera had been isolated previously from comparable sources. The isolates were affiliated with Alpha- and Gammaproteobacteria, Bacilli, and Actinobacteria. A comparable large portion of up to 22 isolates, i.e., 15 phylotypes, probably represent new species. Likewise, 47 isolates (approximately 50%) displayed antibiotic activities, mostly against grampositive indicator strains. Of the active strains, 63.8 % had antibiotic traits only on one or two of the growth media, whereas only 12.7 % inhibited growth on five or all six media. The application of six different media for antimicrobial testing resulted in twice the number of positive hits as obtained with only a single medium. The use of different media for the isolation of bacteria as well as the variation of media considered suitable for the production of antibiotic substances significantly enhanced both the number of isolates obtained and the proportion of antibiotic active cultures. Thus the approach described herein offers an improved strategy in the search for new antibiotic compounds.

Mischaracterizing social psychology to support the laudable goal of increasing its political diversity.

Science.gov (United States)

Eagly, Alice H

2015-01-01

Duarte et al.'s arguments for increasing political diversity in social psychology are based on mischaracterizations of social psychology as fundamentally flawed in understanding stereotype accuracy and the effects of attitudes on information processing. I correct their misunderstandings while agreeing with their view that political diversity, along with other forms of diversity, stands to benefit social psychology.

The diversity, extracellular enzymatic activities and photoprotective compounds of yeasts isolated in Antarctica

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Aline B. M Vaz

2011-09-01

Full Text Available The diversity of yeasts collected from different sites in Antarctica (Admiralty Bay, King George Island and Port Foster Bay and Deception Island and their ability to produce extracellular enzymes and mycosporines were studied. Samples were collected during the austral summer season, between November 2006 and January 2007, from the rhizosphere of Deschampsia antarctica, ornithogenic (penguin guano soil, soil, marine and lake sediments, marine water and freshwater from lakes. A total of 89 isolates belonging to the following genera were recovered: Bensingtonia, Candida, Cryptococcus, Debaryomyces, Dioszegia, Exophiala, Filobasidium, Issatchenkia (Pichia, Kodamaea, Leucosporidium, Leucosporidiella, Metschnikowia, Nadsonia, Pichia, Rhodotorula, and Sporidiobolus, and the yeast-like fungi Aureobasidium, Leuconeurospora and Microglossum. Cryptococcus victoriae was the most frequently identified species. Several species isolated in our study have been previously reported to be Antarctic psychophilic yeasts, including Cr. antarcticus, Cr. victoriae, Dioszegia hungarica and Leucosporidium scottii. The cosmopolitan yeast species A. pullulans, C. zeylanoides, D. hansenii, I. orientalis, K. ohmeri, P. guilliermondii, Rh. mucilaginosa, and S. salmonicolor were also isolated. Five possible new species were identified. Sixty percent of the yeasts had at least one detectable extracellular enzymatic activity. Cryptococcus antarcticus, D. aurantiaca, D. crocea, D. hungarica, Dioszegia sp., E. xenobiotica, Rh. glaciales, Rh. laryngis, Microglossum sp. 1 and Microglossum sp. 2 produced mycosporines. Of the yeast isolates, 41.7% produced pigments and/or mycosporines and could be considered adapted to survive in Antarctica. Most of the yeasts had extracellular enzymatic activities at 4ºC and 20ºC, indicating that they could be metabolically active in the sampled substrates.

Social isolation induces autophagy in the mouse mammary gland: link to increased mammary cancer risk.

Science.gov (United States)

Sumis, Allison; Cook, Katherine L; Andrade, Fabia O; Hu, Rong; Kidney, Emma; Zhang, Xiyuan; Kim, Dominic; Carney, Elissa; Nguyen, Nguyen; Yu, Wei; Bouker, Kerrie B; Cruz, Idalia; Clarke, Robert; Hilakivi-Clarke, Leena

2016-10-01

Social isolation is a strong predictor of early all-cause mortality and consistently increases breast cancer risk in both women and animal models. Because social isolation increases body weight, we compared its effects to those caused by a consumption of obesity-inducing diet (OID) in C57BL/6 mice. Social isolation and OID impaired insulin and glucose sensitivity. In socially isolated, OID-fed mice (I-OID), insulin resistance was linked to reduced Pparg expression and increased neuropeptide Y levels, but in group-housed OID fed mice (G-OID), it was linked to increased leptin and reduced adiponectin levels, indicating that the pathways leading to insulin resistance are different. Carcinogen-induced mammary tumorigenesis was significantly higher in I-OID mice than in the other groups, but cancer risk was also increased in socially isolated, control diet-fed mice (I-C) and G-OID mice compared with that in controls. Unfolded protein response (UPR) signaling (GRP78; IRE1) was upregulated in the mammary glands of OID-fed mice, but not in control diet-fed, socially isolated I-C mice. In contrast, expression of BECLIN1, ATG7 and LC3II were increased, and p62 was downregulated by social isolation, indicating increased autophagy. In the mammary glands of socially isolated mice, but not in G-OID mice, mRNA expressions of p53 and the p53-regulated autophagy inducer Dram1 were upregulated, and nuclear p53 staining was strong. Our findings further indicated that autophagy and tumorigenesis were not increased in Atg7(+/-) mice kept in social isolation and fed OID. Thus, social isolation may increase breast cancer risk by inducing autophagy, independent of changes in body weight. © 2016 Society for Endocrinology.

Molecular Comparison and Evolutionary Analyses of VP1 Nucleotide Sequences of New African Human Enterovirus 71 Isolates Reveal a Wide Genetic Diversity

Science.gov (United States)

Nougairède, Antoine; Joffret, Marie-Line; Deshpande, Jagadish M.; Dubot-Pérès, Audrey; Héraud, Jean-Michel

2014-01-01

Most circulating strains of Human enterovirus 71 (EV-A71) have been classified primarily into three genogroups (A to C) on the basis of genetic divergence between the 1D gene, which encodes the VP1 capsid protein. The aim of the present study was to provide further insights into the diversity of the EV-A71 genogroups following the recent description of highly divergent isolates, in particular those from African countries, including Madagascar. We classified recent EV-A71 isolates by a large comparison of 3,346 VP1 nucleotidic sequences collected from GenBank. Analysis of genetic distances and phylogenetic investigations indicated that some recently-reported isolates did not fall into the genogroups A-C and clustered into three additional genogroups, including one Indian genogroup (genogroup D) and 2 African ones (E and F). Our Bayesian phylogenetic analysis provided consistent data showing that the genogroup D isolates share a recent common ancestor with the members of genogroup E, while the isolates of genogroup F evolved from a recent common ancestor shared with the members of the genogroup B. Our results reveal the wide diversity that exists among EV-A71 isolates and suggest that the number of circulating genogroups is probably underestimated, particularly in developing countries where EV-A71 epidemiology has been poorly studied. PMID:24598878

Genetic diversity of merozoite surface protein-2 in Plasmodium falciparum isolates from Aceh province, Indonesia

Science.gov (United States)

Jamil, K. F.; Supargiyono, S.; Syafruddin, D.; Pratama, N.; Silvy, S.

2018-03-01

Estimated 3.3 million Indonesian population were infected with malaria. However, extensive genetic polymorphism of the field isolates MSP-2 of P. falciparum represents a major obstacle for the development of malaria treatment. The aim of this study to investigate the genetic diversity of MSP-2 genotype in field isolates of P. falciparum collected in Aceh Province. A total of 90 patients enrolled in this study who were selected from positive malaria from eleven district Hospitals in Aceh from 2013-2015. Data was collected by anamnesis, complete physical examination and laboratory tests for MSP-2. All protocol to diagnose malaria assigned following the WHO 2010 guideline. All samples were stored in Eijkman Biology Molecular Institute, Jakarta.Among 90 samples were 57.7% male and 42.3% female with the most cases ages between 21-30 years old. Allele typing analysis displayed the polymorphic nature of P. falciparum. The MSP-2 have two alleles, 62.2% (56/90) for FC27 type and 58.9% (53/90) for 3D7 type and 21.2% (19/90) for mixed FC27 and 3D7 infection were identified. Diverse allele types from Aceh Province was identified in MSP-2 P. falciparum patients; there is the almost similar number of patients infected with both allele. A moderate level of the mixed allele was also observed.

Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides.

Science.gov (United States)

Brown, Steven D; Utturkar, Sagar M; Klingeman, Dawn M; Johnson, Courtney M; Martin, Stanton L; Land, Miriam L; Lu, Tse-Yuan S; Schadt, Christopher W; Doktycz, Mitchel J; Pelletier, Dale A

2012-11-01

To aid in the investigation of the Populus deltoides microbiome, we generated draft genome sequences for 21 Pseudomonas strains and 19 other diverse bacteria isolated from Populus deltoides roots. Genome sequences for isolates similar to Acidovorax, Bradyrhizobium, Brevibacillus, Caulobacter, Chryseobacterium, Flavobacterium, Herbaspirillum, Novosphingobium, Pantoea, Phyllobacterium, Polaromonas, Rhizobium, Sphingobium, and Variovorax were generated.

Insight into Antigenic Diversity of VAR2CSA-DBL5 epsilon Domain from Multiple Plasmodium falciparum Placental Isolates

DEFF Research Database (Denmark)

Gnidehou, Sedami; Jessen, Leon Ivar; Gangnard, Stephane

2010-01-01

on the surface of placental parasites. Despite high DBL5e sequence homology among parasite isolates, sequence analyses identified motifs in DBL5e that discriminate parasites according to donor's parity. Moreover, recombinant proteins of two VAR2CSA DBL5e variants displayed diverse recognition patterns by plasma...... from malaria-exposed women, and diverse proteoglycan binding abilities. Conclusions/Significance: This study provides insights into conserved and exposed B cell epitopes in DBL5e that might be a focus for cross reactivity. The importance of sequence variation in VAR2CSA as a critical challenge...

Plasmodium falciparum: genetic diversity and complexity of infections in an isolated village in western Thailand.

Science.gov (United States)

Tanabe, Kazuyuki; Zollner, Gabriela; Vaughan, Jefferson A; Sattabongkot, Jetsumon; Khuntirat, Benjawan; Honma, Hajime; Mita, Toshihiro; Tsuboi, Takafumi; Coleman, Russell

2015-06-01

Genetic diversity of Plasmodium falciparum is intimately associated with morbidity, mortality and malaria control strategies. It is therefore imperative to study genetic makeup and population structure of this parasite in endemic areas. In Kong Mong Tha, an isolated village in western Thailand, the majority of P. falciparum infections are asymptomatic. In this study we investigated complexity of infections and single nucleotide polymorphisms (SNPs) in the P. falciparum population of Kong Mong Tha, and compared results with those previously obtained from Mae Sod, in northwestern Thailand, where the majority of infections were symptomatic. Using PCR-based determination of the 5' merozoite surface protein 1 gene (msp1) recombinant types, we found that 39% of 59 P. falciparum isolates from Kong Mong Tha had multiple 5' recombinant types with a mean number of 1.54. These values were much lower than those obtained from Mae Sod: 96% for multiple infections and with a mean number of 3.61. Analysis of full-length sequences of two housekeeping genes, the P-type Ca(2+)-transporting ATPase gene (n=33) plus adenylosuccinate lyase gene (n=33), and three vaccine candidate antigen genes, msp1 (n=26), the circumsporozoite protein gene, csp (n=30) and the apical membrane antigen 1 gene, ama 1 (n=32), revealed that in all of these genes within-population SNP diversity was at similar levels between Kong Mong Tha and Mae Sod, suggesting that the extent of MOI and clinical manifestations of malaria are not strongly associated with genetic diversity. Additionally, we did not detect significant genetic differentiation between the two parasite populations, as estimated by the Wright's fixation index of inter-population variance in allele frequencies, suggesting that gene flow prevented the formation of population structuring. Thus, this study highlights unique features of P. falciparum populations in Thailand. The implications of these finding are discussed. © 2013.

Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus deltoides

Energy Technology Data Exchange (ETDEWEB)

Brown, Steven D [ORNL; Utturkar, Sagar M [ORNL; Klingeman, Dawn Marie [ORNL; Johnson, Courtney M [ORNL; Martin, Stanton [ORNL; Land, Miriam L [ORNL; Lu, Tse-Yuan [ORNL; Schadt, Christopher Warren [ORNL; Doktycz, Mitchel John [ORNL; Pelletier, Dale A [ORNL

2012-01-01

To aid in the investigation of the Populus deltoides microbiome we generated draft genome sequences for twenty one Pseudomonas and twenty one other diverse bacteria isolated from Populus deltoides roots. Genome sequences for isolates similar to Acidovorax, Bradyrhizobium, Brevibacillus, Burkholderia, Caulobacter, Chryseobacterium, Flavobacterium, Herbaspirillum, Novosphingobium, Pantoea, Phyllobacterium, Polaromonas, Rhizobium, Sphingobium and Variovorax were generated.

Studying genetic diversity of whitefly B. tabaci Egyptian isolates in relation to some worldwide isolates

Directory of Open Access Journals (Sweden)

Inas Farouk Fahmy

2015-06-01

Full Text Available Bemisia tabaci (Gennadius (Hemiptera, Aleyrodidae is considered to be one of the most damaging pests in agriculture, causing severe losses in crops worldwide, affecting the tropical and subtropical regions. Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR was used to assess the genetic diversity between different isolates collected from different regions in Egypt compared with some other worldwide isolates of this insect pest. Out of 12 primers 8 primers from Operon technology have shown to differentiate between 13 collected B. tabaci samples from all over Egypt and some other samples collected from different countries with two other populations representing biotypes A and B collected from the US used for biotype demarcation. Using 13 insect samples, RAPD analysis has produced a total number of 72 markers; about 68 polymorphic markers were revealed. The total number of bands obtained for each primer ranged from 4 to 14 within an average of 9 bands per primer. Of the pair wise combination among fifteen populations Ismailia population showed the highest similarity index (0.947, while US biotype A scored the lowest similarity index (0.326. Two major clusters were formed from the UPGMA dendrogram, which was constructed based on Dice similarity coefficient. RAPD-PCR screening demarcated the whitefly population based on the host species and genetic biotypes. Two major clusters have been revealed as A and B with two other minor clusters A1, A2, and B1, B2. Most of the samples collected from Egypt were clustered together in a minor cluster named A1. A1 group is divided into two sub-groups. A1a comprises the populations from Beni-Sweif in Upper Egypt, Ismailia, Kalyobia, El-Fayoum, Tanta, Kafr El-Sheikh, Alexandria, and A1b comprises Spain and Sudan. Group A1a is clustered together based on their host which belongs to the Cucurbitaceae family while Alexandria was separated individually based on its host which is cauliflower. Through

Creativity in gifted identification: increasing accuracy and diversity.

Science.gov (United States)

Luria, Sarah R; O'Brien, Rebecca L; Kaufman, James C

2016-08-01

Many federal definitions and popular theories of giftedness specify creativity as a core component. Nevertheless, states rely primarily on measures of intelligence for giftedness identification. As minority and culturally diverse students continue to be underrepresented in gifted programs, it is reasonable to ask if increasing the prominence of creativity in gifted identification may help increase balance and equity. In this paper, we explore both layperson and psychometric conceptions of bias and suggest that adding creativity measures to the identification process alleviates both perceptions and the presence of bias. We recognize, however, the logistic and measurement-related challenges to including creativity assessments. © 2016 New York Academy of Sciences.

Diversity and antimicrobial susceptibility of oxytetracycline-resistant isolates of Stenotrophomonas sp. and Serratia sp. associated with Costa Rican crops.

Science.gov (United States)

Rodríguez, C; Wachlin, A; Altendorf, K; García, F; Lipski, A

2007-12-01

To ameliorate the identification, evaluate the diversity, and determine the antimicrobial sensitivity of 19 oxytetracycline-resistant isolates of Stenotrophomonas sp. and Serratia sp. associated with Costa Rican crops. Phenotypical, chemotaxonomical, and molecular data allocated most isolates to the species Sten. maltophilia and Ser. marcescens. The API profiles, antimicrobial resistance patterns (ATB system), and BOX-polymerase chain reaction (PCR) genomic fingerprints of isolates of Stenotrophomonas sp. exhibited a higher degree of heterogeneity than those obtained for the isolates of Serratia sp. The former group of bacteria exhibited multiresistance to antimicrobials. In contrast, isolates of Serratia sp. were sensitive to the majority of the drugs tested. Changes in the results of the antibiograms throughout incubation, which indicate an induction of tolerance, were observed for isolates of both the species. Minimum inhibitory concentration of oxytetracycline, determined using E-test stripes, were rather elevated. The occurrence of two species of opportunistic pathogens in crop-associated materials poses a risk to consumers in the community. The phenotypic and genotypic data presented could support epidemiologist and physicians dealing with infections caused by environmental strains of these taxa.

Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust

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Ulisses eNunes da Rocha

2015-04-01

Full Text Available Biological Soil Crusts (BSCs are organosedimentary assemblages comprised of microbes and minerals in topsoil of terrestrial environments. BSCs strongly impact soil quality in dryland ecosystems (e.g., soil structure and nutrient yields due to pioneer species such as Microcoleus vaginatus; phototrophs that produce filaments that bind the soil together, and support an array of heterotrophic microorganisms. These microorganisms in turn contribute to soil stability and biogeochemistry of BSCs. Non-cyanobacterial populations of BSCs are less well known than cyanobacterial populations. Therefore, we attempted to isolate a broad range of numerically significant and phylogenetically representative BSC aerobic heterotrophs. Combining simple pre-treatments (hydration of BSCs under dark and light and isolation strategies (media with varying nutrient availability and protection from oxidative stress we recovered 402 bacterial and one fungal isolate in axenic culture, which comprised 116 phylotypes (at 97% 16S rRNA gene sequence homology, 115 bacterial and one fungal. Each medium enriched a mostly distinct subset of phylotypes, and cultivated phylotypes varied due to the BSC pre-treatment. The fraction of the total phylotype diversity isolated, weighted by relative abundance in the community, was determined by the overlap between isolate sequences and OTUs reconstructed from metagenome or metatranscriptome reads. Together, more than 8% of relative abundance of OTUs in the metagenome was represented by our isolates, a cultivation efficiency much larger than typically expected from most soils. We conclude that simple cultivation procedures combined with specific pre-treatment of samples afford a significant reduction in the culturability gap, enabling physiological and metabolic assays that rely on ecologically relevant axenic cultures.

Increased dopaminergic activity in socially isolated rats: an electrophysiological study

DEFF Research Database (Denmark)

Fabricius, Katrine; Helboe, Lone; Fink-Jensen, Anders

2010-01-01

The development of animal models mimicking symptoms associated with schizophrenia has been a critical step in understanding the neurobiological mechanisms underlying the disease. Long-term social isolation from weaning in rodents, a model based on the neurodevelopmental hypothesis of schizophrenia......, has been suggested to mimic some of the deficits seen in schizophrenic patients. We confirm in the present study that socially isolated rats display an increase in both spontaneous and d-amphetamine-induced locomotor activity, as well as deficits in sensorimotor gating as assessed in a pre......, and a change of firing activity towards a more irregular and bursting firing pattern. Taken together, our findings suggest that the behavioral phenotype induced by social isolation may be driven by an overactive dopamine system....

Evolution of increased phenotypic diversity enhances population performance by reducing sexual harassment in damselflies.

Science.gov (United States)

Takahashi, Yuma; Kagawa, Kotaro; Svensson, Erik I; Kawata, Masakado

2014-07-18

The effect of evolutionary changes in traits and phenotypic/genetic diversity on ecological dynamics has received much theoretical attention; however, the mechanisms and ecological consequences are usually unknown. Female-limited colour polymorphism in damselflies is a counter-adaptation to male mating harassment, and thus, is expected to alter population dynamics through relaxing sexual conflict. Here we show the side effect of the evolution of female morph diversity on population performance (for example, population productivity and sustainability) in damselflies. Our theoretical model incorporating key features of the sexual interaction predicts that the evolution of increased phenotypic diversity will reduce overall fitness costs to females from sexual conflict, which in turn will increase productivity, density and stability of a population. Field data and mesocosm experiments support these model predictions. Our study suggests that increased phenotypic diversity can enhance population performance that can potentially reduce extinction rates and thereby influence macroevolutionary processes.

Pathogenic diversity of Sclerotium rolfsii isolates, a potential ...

African Journals Online (AJOL)

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et al., 2002; Shukla and Pandey, 2007). Therefore, present investigation was carried out to study the pathogenic varia- bility and justify the separate identity of the S. rolfsii isolates associated with Parthenium. MATERIALS AND METHODS. Test isolates and their maintenance. Ten isolates of S. rolfsii incites collar rot disease ...

Immigration Ethnic Diversity and Political Outcomes: Evidence from Denmark

DEFF Research Database (Denmark)

Harmon, Nikolaj Arpe

I study the impact of immigration and increasing ethnic diversity on political outcomes in immigrant-receiving countries, focusing on immigration and election outcomes in Danish municipalities 1981-2001. A rich set of control variables isolates ethnic diversity effects from those of other immigrant...... characteristics and a novel IV strategy based on historical housing stock data addresses issues of endogenous location choices of immigrants. Increases in local ethnic diversity lead to right-ward shifts in election outcomes by shifting electoral support away from traditional "big government" left-wing parties...... and towards anti-immigrant nationalist parties in particular. These effects appear in both local and national elections....

Diversity and antibiotic susceptibility of autochthonous dairy enterococci isolates: Are they safe candidates for autochthonous starter cultures?

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Amarela eTerzić-Vidojević

2015-09-01

Full Text Available Enterococci represent the most controversial group of dairy bacteria. They are found to be the main constituent of many traditional Mediterranean dairy products and contribute to their characteristic taste and flavor. On the other hand, during the last 50 years antibiotic-resistant enterococci have emerged as leading causes of nosocomial infections worldwide. The aim of this study was to determine the diversity, technological properties, antibiotic susceptibility and virulence traits of 636 enterococci previously isolated from 55 artisan dairy products from 12 locations in the Western Balkan countries of Serbia, Croatia and Bosnia and Herzegovina. All strains were identified both by microbiological and molecular methods. The predominant species was Enterococcus durans, followed by E. faecalis and E. faecium. Over 44% of the isolates were resistant to ciprofloxacin and erythromycin, while 26.2% of the isolates were multi-resistant to three or more antibiotics belonging to different families. 185 isolates (29.1% were susceptible to all 13 of the antibiotics tested. The antibiotic-susceptible isolates were further tested for possible virulence genes and the production of biogenic amines. Finally, five enterococci isolates were found to be antibiotic susceptible with good technological characteristics and without virulence traits or the ability to produce biogenic amines, making them possible candidates for biotechnological application as starter cultures in the dairy industry.

Diverse bacteria isolated from microtherm oil-production water.

Science.gov (United States)

Sun, Ji-Quan; Xu, Lian; Zhang, Zhao; Li, Yan; Tang, Yue-Qin; Wu, Xiao-Lei

2014-02-01

In total, 435 pure bacterial strains were isolated from microtherm oil-production water from the Karamay Oilfield, Xinjiang, China, by using four media: oil-production water medium (Cai medium), oil-production water supplemented with mineral salt medium (CW medium), oil-production water supplemented with yeast extract medium (CY medium), and blood agar medium (X medium). The bacterial isolates were affiliated with 61 phylogenetic groups that belong to 32 genera in the phyla Actinobacteria, Firmicutes, and Proteobacteria. Except for the Rhizobium, Dietzia, and Pseudomonas strains that were isolated using all the four media, using different media led to the isolation of bacteria with different functions. Similarly, nonheme diiron alkane monooxygenase genes (alkB/alkM) also clustered according to the isolation medium. Among the bacterial strains, more than 24 % of the isolates could use n-hexadecane as the sole carbon source for growth. For the first time, the alkane-degrading ability and alkB/alkM were detected in Rhizobium, Rhodobacter, Trichococcus, Micrococcus, Enterococcus, and Bavariicoccus strains, and the alkM gene was detected in Firmicutes strains.

Rapid isolation of gene homologs across taxa: Efficient identification and isolation of gene orthologs from non-model organism genomes, a technical report

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Heffer Alison

2011-03-01

Full Text Available Abstract Background Tremendous progress has been made in the field of evo-devo through comparisons of related genes from diverse taxa. While the vast number of species in nature precludes a complete analysis of the molecular evolution of even one single gene family, this would not be necessary to understand fundamental mechanisms underlying gene evolution if experiments could be designed to systematically sample representative points along the path of established phylogenies to trace changes in regulatory and coding gene sequence. This isolation of homologous genes from phylogenetically diverse, representative species can be challenging, especially if the gene is under weak selective pressure and evolving rapidly. Results Here we present an approach - Rapid Isolation of Gene Homologs across Taxa (RIGHT - to efficiently isolate specific members of gene families. RIGHT is based upon modification and a combination of degenerate polymerase chain reaction (PCR and gene-specific amplified fragment length polymorphism (AFLP. It allows targeted isolation of specific gene family members from any organism, only requiring genomic DNA. We describe this approach and how we used it to isolate members of several different gene families from diverse arthropods spanning millions of years of evolution. Conclusions RIGHT facilitates systematic isolation of one gene from large gene families. It allows for efficient gene isolation without whole genome sequencing, RNA extraction, or culturing of non-model organisms. RIGHT will be a generally useful method for isolation of orthologs from both distant and closely related species, increasing sample size and facilitating the tracking of molecular evolution of gene families and regulatory networks across the tree of life.

GENETIC DIVERSITY OF Vibrio harveyi ISOLATED FROM TIGER PRAWN Penaeus monodon HATCHERIES AND GROW OUT PONDS

OpenAIRE

Muliani Muliani; Ince Ayu Khairana Kadriah; Andi Parenrengi; Sulaeman Sulaeman

2006-01-01

ibrio harveyi is known as one among the most harmful bacteria infecting tiger prawn at every stage of its life’s. The present research was aimed to reveal the genetic diversity of Vibrio harveyi isolated from tiger prawn (Penaeus monodon) culture. The samples of bacteria were collected from hatchery (brood-stock, larvae, natural feed, artemia, and larval rearing water) and grow-out (juveniles, water, shrimp, sediment, plankton, crab, mollusc, microalgae, and wild fish).  The taxonomic identif...

Life on the margin: genetic isolation and diversity loss in a peripheral marine ecosystem, the Baltic Sea.

Science.gov (United States)

Johannesson, Kerstin; André, Carl

2006-07-01

Marginal populations are often isolated and under extreme selection pressures resulting in anomalous genetics. Consequently, ecosystems that are geographically and ecologically marginal might have a large share of genetically atypical populations, in need of particular concern in management of these ecosystems. To test this prediction, we analysed genetic data from 29 species inhabiting the low saline Baltic Sea, a geographically and ecologically marginal ecosystem. On average Baltic populations had lost genetic diversity compared to Atlantic populations: a pattern unrelated to dispersal capacity, generation time of species and taxonomic group of organism, but strongly related to type of genetic marker (mitochondrial DNA loci had lost c. 50% diversity, and nuclear loci 10%). Analyses of genetic isolation by geographic distance revealed clinal patterns of differentiation between Baltic and Atlantic regions. For a majority of species, clines were sigmoid with a sharp slope around the Baltic Sea entrance, indicating impeded gene flows between Baltic and Atlantic populations. Some species showed signs of allele frequencies being perturbed at the edge of their distribution inside the Baltic Sea. Despite the short geological history of the Baltic Sea (8000 years), populations inhabiting the Baltic have evolved substantially different from Atlantic populations, probably as a consequence of isolation and bottlenecks, as well as selection on adaptive traits. In addition, the Baltic Sea also acts a refuge for unique evolutionary lineages. This marginal ecosystem is thus vulnerable but also exceedingly valuable, housing unique genes, genotypes and populations that constitute an important genetic resource for management and conservation.

Trajectories of Neighborhood Change : Spatial Patterns of Increasing Ethnic Diversity

NARCIS (Netherlands)

Zwiers, M.D.; van Ham, M.; Manley, D.J.

Western cities are increasingly ethnically diverse and in most cities the share of ethnic minorities is growing. Studies analyzing changing ethnic geographies often limit their analysis to changes in ethnic concentrations in neighborhoods between two points in time. Such a static approach limits our

Genetic diversity of Aspergillus fumigatus in indoor hospital environments.

Science.gov (United States)

Araujo, Ricardo; Amorim, António; Gusmão, Leonor

2010-09-01

Environmental isolates of Aspergillus fumigatus are less studied than those recovered from clinical sources. In the present study, the genetic diversity among such environmental isolates was assessed, as well as their dispersion ability and the acquisition of new strains in 19 medical units of the same hospital. A. fumigatus isolates were genotyped using a single multiplex PCR-based reaction with eight microsatellite markers and an insertion/deletion polymorphism. A total of 130 unique genotypes were found among a total of 250 A. fumigatus isolates. Genotypic diversity ranged from 0.86 to 1 in samples from hospital rooms, and there was no correlation between these samples and the presence of high-efficiency particulate air filters or any other air filtration system. Four of the six most prevalent A. fumigatus strains were recovered from water samples. The occurrence of microvariation was common among environmental isolates, which affected each of the microsatellite markers. The assessment of the genetic diversity of A. fumigatus is a useful tool for illustrating the presence or absence of specific clonal populations in a clinical setting. A. fumigatus populations were highly dynamic indoors, and new populations were found in just a few months. Due to the high indoor dispersion capability of A. fumigatus, more attention should be given to strains with increased pathogenic potential or reduced susceptibility to anti-fungal drugs.

Extraordinary Diversity of Immune Response Proteins among Sea Urchins: Nickel-Isolated Sp185/333 Proteins Show Broad Variations in Size and Charge

Science.gov (United States)

Sherman, Lauren S.; Schrankel, Catherine S.; Brown, Kristy J.; Smith, L. Courtney

2015-01-01

Effective protection against pathogens requires the host to produce a wide range of immune effector proteins. The Sp185/333 gene family, which is expressed by the California purple sea urchin Strongylocentrotus purpuratus in response to bacterial infection, encodes a highly diverse repertoire of anti-pathogen proteins. A subset of these proteins can be isolated by affinity to metal ions based on multiple histidines, resulting in one to four bands of unique molecular weight on standard Western blots, which vary depending on the individual sea urchin. Two dimensional gel electrophoresis (2DE) of nickel-isolated protein samples followed by Western blot was employed to detect nickel-isolated Sp185/333 (Ni-Sp185/333) proteins and to evaluate protein diversity in animals before and after immune challenge with marine bacteria. Ni-Sp185/333 proteins of the same molecular weight on standard Western blots appear as a broad complex of variants that differ in pI on 2DE Western blots. The Ni-Sp185/333 protein repertoire is variable among animals, and shows a variety of changes among individual sea urchins in response to immune challenges with both the same and different species of bacteria. The extraordinary diversity of the Ni-Sp185/333 proteins may provide significant anti-pathogen capabilities for sea urchins that survive solely on innate immunity. PMID:26406912

The heterogeneity of socially isolated older adults: a social isolation typology.

Science.gov (United States)

Machielse, Anja

2015-01-01

Recent statistics show a growing number of older adults who are living alone and are socially isolated. It is against this background that, in recent years, many interventions have been developed to address social isolation among the elderly. Evaluative studies show that most interventions are hardly effective, though. An important reason for this is the heterogeneity of the socially isolated. This article offers insight into this heterogeneity by presenting a typology with different profiles of socially isolated older adults and the intervention implications of this typology. The typology is derived from an extensive qualitative study on socially isolated elderly individuals in the Netherlands. The typology imposes some degree of order to a diversity of circumstances, ambitions, and possibilities of the socially isolated elderly, thereby deepening the understanding of the heterogeneity of this population. The definition of social isolation used in this study starts from a societal angle of incidence, namely the current policy context of Western European welfare states, in which governments emphasize the importance of independence and self-reliance of their citizens. Developed from that perspective, the typology provides a theoretical basis for applying interventions aimed at increasing self-reliance of social isolated elderly. This perspective on social isolation also has consequences for the way in which the effectiveness of interventions to alleviate social isolation is assessed.

Genetic diversity of Aspergillus species isolated from onychomycosis and Aspergillus hongkongensis sp. nov., with implications to antifungal susceptibility testing.

Science.gov (United States)

Tsang, Chi-Ching; Hui, Teresa W S; Lee, Kim-Chung; Chen, Jonathan H K; Ngan, Antonio H Y; Tam, Emily W T; Chan, Jasper F W; Wu, Andrea L; Cheung, Mei; Tse, Brian P H; Wu, Alan K L; Lai, Christopher K C; Tsang, Dominic N C; Que, Tak-Lun; Lam, Ching-Wan; Yuen, Kwok-Yung; Lau, Susanna K P; Woo, Patrick C Y

2016-02-01

Thirteen Aspergillus isolates recovered from nails of 13 patients (fingernails, n=2; toenails, n=11) with onychomycosis were characterized. Twelve strains were identified by multilocus sequencing as Aspergillus spp. (Aspergillus sydowii [n=4], Aspergillus welwitschiae [n=3], Aspergillus terreus [n=2], Aspergillus flavus [n=1], Aspergillus tubingensis [n=1], and Aspergillus unguis [n=1]). Isolates of A. terreus, A. flavus, and A. unguis were also identifiable by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The 13th isolate (HKU49(T)) possessed unique morphological characteristics different from other Aspergillus spp. Molecular characterization also unambiguously showed that HKU49(T) was distinct from other Aspergillus spp. We propose the novel species Aspergillus hongkongensis to describe this previously unknown fungus. Antifungal susceptibility testing showed most Aspergillus isolates had low MICs against itraconazole and voriconazole, but all Aspergillus isolates had high MICs against fluconazole. A diverse spectrum of Aspergillus species is associated with onychomycosis. Itraconazole and voriconazole are probably better drug options for Aspergillus onychomycosis. Copyright © 2016 Elsevier Inc. All rights reserved.

Do Pine Trees in Aspen Stands Increase Bird Diversity

OpenAIRE

Rumble, Mark A; Mills, Todd R; Dystra, Brian L; Flake, Lester D

2001-01-01

In the Black Hills of South Dakota, quaking aspen (Populus tremuloides) is being replaced by conifers through fire suppression and successional processes. Al- though the Black Hills National forest is removing conifers (primarily ponderosa pine [Pinus ponderosa])toincreasetheaspencommunitiesinsomemixedstands,ForestPlan guidelines allow four conifers per hectare to remain to increase diversity in the remaining aspen stand. We compared bird species richness in pure ponderosa pine, mixed stands ...

Genetic diversity of six isolated populations of the leopard moth, Zeuzera pyrina (Lep: Zeuzeridae

Directory of Open Access Journals (Sweden)

Raheleh Dolati

2017-03-01

Full Text Available The leopard moth, Zeuzera pyrina (Lep: Zeuzeridae, is an important pest of a wide range of trees and shrubs including walnut and apple across the world. The natural populations of the leopard moth in different geographical areas of Iran show significant differences in some of their biological characteristics such as time of emergence, generation time and host specificity. So, we hypothesized that these populations may represent different subspecies that move toward a speciation event in their evolutionary route. In this study, we evaluated the genetic diversity of six different geographically isolated populations of the leopard moth using the sequence alignment of cytochrome oxidase c subunit one (COI. A fragment of 642 base pairs was amplified in all six populations and the phylogenetic tree was created based on sequenced fragments. Our results revealed significant differences in the nucleotide sequence of COI gene in these populations. Differences in climatic conditions of these regions seem to be the most powerful force driving this diversity among the studied populations.

Increasing Diversity in the Earth Sciences (IDES) - An Oregon Effort

Science.gov (United States)

de Silva, S. L.; Duncan, R. A.; Wright, D. J.; de Silva, L.; Guerrero, E. F.

2011-12-01

The IDES (Increasing Diversity in Earth Sciences) Program is the first partnership of its kind in the state of Oregon targeted at broadening participation in the Earth Science enterprise. Funded by the National Science Foundation Opportunities to Enhance Diversity in the Geosciences program (NSF-OEDG), this partnership involves community colleges, a research university with major strengths in Earth Science research and education and an institutionalized commitment to enhancing diversity, state and federal agencies, centers of informal education, and the Oregon Space Grant Consortium, IDES has two integrated goals: 1) to increase the number of students from under-represented groups who pursue careers in Earth Science research and education, and 2) to strengthen the understanding of Earth Sciences and their relevance to society among broad and diverse segments of the population. Built around the best practices of tiered mentoring, interactive student cohort, research and education internships, and financial support, this 4-year program recruits 10 to 12 students (mainly rising juniors) each year from science majors at Oregon State University and five Oregon community colleges. The program is reaching its goals by: a) training participants in the application of geospatial to Earth Science problems of personal relevance b) immersing participants in a two-year mentored research project that involves summer internships with academic units, state and federal agencies, and centers for informal education in Oregon. c) exposing, educating, and involving participants in the breadth of Earth Science careers through contact with Earth Science professionals through mentors, a professional internship, and a learning community that includes a speaker series. d) instilling an understanding of context and relevance of the Earth Science Enterprise to the participants, their families, their communities, and the general public. We report on the first two years of this program during

Pro-inflammatory Cytokine Response and Genetic Diversity in Merozoite Surface Protein 2 of Plasmodium falciparum Isolates from Nigeria.

Science.gov (United States)

Ajibaye, Olusola; Osuntoki, Akinniyi A; Ebuehi, Albert Ot; Iwalokun, Bamidele A; Balogun, Emmanuel O; Egbuna, Kathleen N

2017-01-01

Polymorphisms in Plasmodium falciparum merozoite surface protein-2 ( msp -2) and associated parasite genetic diversity which varies between malaria-endemic regions remain a limitation in malaria vaccine development. Pro-inflammatory cytokines are important in immunity against malaria, understanding the influence of genetic diversity on cytokine response is important for effective vaccine design. P. falciparum isolates obtained from 300 Nigerians with uncomplicated falciparum malaria at Ijede General Hospital, Ijede (IJE), General Hospital Ajeromi, Ajeromi (AJE) and Saint Kizito Mission Hospital, Lekki, were genotyped by nested polymerase chain reaction of msp -2 block 3 while ELISA was used to determine the pro-inflammatory cytokine response to describe the genetic diversity of P. falciparum . Eighteen alleles were observed for msp -2 loci. Of the 195 isolates, 61 (31.0%) had only FC27-type alleles, 38 (19.7%) had only 3D7-type alleles, and 49.3% had multiple parasite lines with both alleles. Band sizes were 275-625 bp for FC27 and 150-425 bp for 3D7. Four alleles were observed from LEK, 2 (375-425 bp) and 2 (275-325 bp) of FC27-and 3D7-types, respectively; 12 alleles from AJE, 9 (275-625 bp) and 3 (325-425 bp) of FC27-types and 3D7-types, respectively; while IJE had a total of 12 alleles, 9 (275-625 bp) and 3 (325-425 bp) of FC27-types and 3D7-types, respectively. Mean multiplicity of infection (MOI) was 1.54. Heterozygosity ( H E ) ranged from 0.77 to 0.87 and was highest for IJE (0.87). Cytokine response was higher among 0.05) but with neither parasite density nor infection type. P. falciparum genetic diversity is extensive in Nigeria, protection via pro-inflammatory cytokines have little or no interplay with infection multiplicity.

Species richness and trophic diversity increase decomposition in a co-evolved food web.

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Benjamin Baiser

Full Text Available Ecological communities show great variation in species richness, composition and food web structure across similar and diverse ecosystems. Knowledge of how this biodiversity relates to ecosystem functioning is important for understanding the maintenance of diversity and the potential effects of species losses and gains on ecosystems. While research often focuses on how variation in species richness influences ecosystem processes, assessing species richness in a food web context can provide further insight into the relationship between diversity and ecosystem functioning and elucidate potential mechanisms underpinning this relationship. Here, we assessed how species richness and trophic diversity affect decomposition rates in a complete aquatic food web: the five trophic level web that occurs within water-filled leaves of the northern pitcher plant, Sarracenia purpurea. We identified a trophic cascade in which top-predators--larvae of the pitcher-plant mosquito--indirectly increased bacterial decomposition by preying on bactivorous protozoa. Our data also revealed a facultative relationship in which larvae of the pitcher-plant midge increased bacterial decomposition by shredding detritus. These important interactions occur only in food webs with high trophic diversity, which in turn only occur in food webs with high species richness. We show that species richness and trophic diversity underlie strong linkages between food web structure and dynamics that influence ecosystem functioning. The importance of trophic diversity and species interactions in determining how biodiversity relates to ecosystem functioning suggests that simply focusing on species richness does not give a complete picture as to how ecosystems may change with the loss or gain of species.

Genetic Diversity in Salmonella Isolates from Ducks and their Environments in Penang, Malaysia using Enterobacterial Repetitive Intergenic Consensus

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Frederick Adzitey 1, Gulam Rusul Rahmat Ali2*, Nurul Huda2 and Rosma Ahmad3

2013-07-01

Full Text Available A total of 107 Salmonella isolates (37 S. typhimurium, 26 S. hadar, 15 S. enteritidis, 15 S. braenderup, and 14 S. albany isolated from ducks and their environments in Penang, Malaysia were typed using enterobacterial repetitive intergenic consensus (ERIC to determine their genetic diversity. Analysis of the Salmonella strains by ERIC produced DNA fingerprints of different sizes for differentiation purposes. The DNA fingerprints or band sizes ranged from 14-8300bp for S. Typhimurium, 146-6593bp for S. hadar, 15-4929bp for S. enteritidis, 14-5142bp for S. braenderup and 7-5712bp for S. albany. Cluster analysis at a coefficient of 0.85 grouped the Salmonella strains into various clusters and singletons. S. typhimurium were grouped into 10 clusters and 6 singletons, S. Hadar were grouped into 3 clusters and 18 singletons, S. enteritidis were grouped into 3 clusters and 7 singletons, S. braenderup were grouped into 4 clusters and 7 singletons, and S. albany were grouped into 3 clusters and 7 singletons with discriminatory index (D ranging from 0.92-0.98. ERIC proved to be a useful typing tool for determining the genetic diversity of the duck Salmonella strains.

Genetic diversity of Streptococcus uberis isolates from dairy cows with subclinical mastitis in Southern Xinjiang Province, China.

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Wang, Lijun; Chen, Wei; Zhang, Lili; Zhu, Yaxin

2013-01-01

Streptococcus uberis is a common cause of dairy cow mastitis throughout the world. The failure to control bovine mastitis caused by S. uberis is largely attributed to the little known about the epidemiology of this bacteria, especially strain differences in the same area. To define the local epidemiology of S. uberis in the south of Xinjiang, China, we explored the genetic diversity of 28 bovine subclinical mastitis field isolates of S. uberis, collected from 3 Chinese farms during 2009 and 2010, which was examined by using pulsed-field gel electrophoresis (PFGE) for clustering of the isolates and multilocus sequence typing (MLST) to assess the relationship between PFGE patterns and to identify genetic lineages. The 28 isolates were grouped into 13 pulsotypes (U1 to U13), and 1 PFGE type (U1) accounted for almost half of the isolates (13/28, 46.4%). This major type was herd specific, indicating either cow-to-cow transmission or infection with isolates from the same environmental reservoirs. The remaining 12 PFGE types of isolates were from different herds, strongly suggesting environmental sources of S. uberis infection. All 28 isolates were analyzed by MLST and clustered into 8 sequence types (STs), of which 7 STs were found to be novel, either with 5 new alleles of 6 housekeeping and virulence genes (ST158, ST159) or with different combinations of previously assigned alleles (ST153, ST154, ST155, ST156, ST157). To our knowledge, this is the first report that documents molecular typing studies of bovine isolates of S. uberis from southern Xinjiang Province, China, which were shown to represent novel genomic backgrounds of this pathogen.

Diversity and antimicrobial susceptibility profiling of staphylococci isolated from bovine mastitis cases and close human contacts.

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Schmidt, T; Kock, M M; Ehlers, M M

2015-09-01

The objectives of this study were to examine the diversity of Staphylococcus spp. recovered from bovine intramammary infections and humans working in close contact with the animals and to evaluate the susceptibility of the staphylococcal isolates to different antimicrobials. A total of 3,387 milk samples and 79 human nasal swabs were collected from 13 sampling sites in the KwaZulu-Natal province of South Africa. In total, 146 Staph. aureus isolates and 102 coagulase-negative staphylococci (CNS) were recovered from clinical and subclinical milk samples. Staphylococcusaureus was isolated from 12 (15.2%) of the human nasal swabs and 95 representative CNS were recovered for further characterization. The CNS were identified using multiplex-PCR assays, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and tuf gene sequencing. Seven Staphylococcus spp. were identified among the CNS of bovine origin, with Staph.chromogenes (78.4%) predominating. The predominant CNS species recovered from the human nasal swabs was Staph.epidermidis (80%) followed by Staph.chromogenes (6.3%). The antimicrobial susceptibility of all staphylococcal isolates was evaluated using disk diffusion and was supplemented by screening for specific antimicrobial resistance genes. Ninety-eight (67.1%) Staph.aureus isolates of bovine origin were pansusceptible; 39 (26.7%) isolates were resistant to a single class, and 7 (4.8%) isolates were resistant to 2 classes of antimicrobials. Two Staph. aureus (1.4%) isolates were multidrug-resistant. Resistance to penicillin was common, with 28.8% of the bovine and 75% of the human Staph. aureus isolates exhibiting resistance. A similar observation was made with the CNS, where 37.3% of the bovine and 89.5% of the human isolates were resistant to penicillin. Multidrug-resistance was common among the human CNS, with 39% of the isolates exhibiting resistance to 3 or more classes of antimicrobials. The antimicrobial

Isolation, Identification, Prevalence, and Genetic Diversity of Bacillus cereus Group Bacteria From Different Foodstuffs in Tunisia.

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Gdoura-Ben Amor, Maroua; Siala, Mariam; Zayani, Mariem; Grosset, Noël; Smaoui, Salma; Messadi-Akrout, Feriele; Baron, Florence; Jan, Sophie; Gautier, Michel; Gdoura, Radhouane

2018-01-01

Bacillus cereus group is widespread in nature and foods. Several members of this group are recognized as causing food spoilage and/or health issues. This study was designed to determine the prevalence and genetic diversity of the B. cereus group strains isolated in Tunisia from different foods (cereals, spices, cooked food, fresh-cut vegetables, raw and cooked poultry meats, seafood, canned, pastry, and dairy products). In total, 687 different samples were collected and searched for the presence of the B. cereus group after selective plating on MYP agar and enumeration of each sample. The typical pink-orange uniform colonies surrounded by a zone of precipitate were assumed to belong to the B. cereus group. One typical colony from each sample was subcultured and preserved as cryoculture. Overall, 191 (27.8%) food samples were found positive, giving rise to a collection of 191 B. cereus -like isolates. The concentration of B. cereus -like bacteria were below 10 3 cfu/g or ml in 77.5% of the tested samples. Higher counts (>10 4 cfu/g or ml) were found in 6.8% of samples including fresh-cut vegetables, cooked foods, cereals, and pastry products. To verify whether B. cereus -like isolates belonged to the B. cereus group, a PCR test targeting the sspE gene sequence specific of the group was carried out. Therefore, 174 isolates were found to be positive. Food samples were contaminated as follows: cereals (67.6%), pastry products (46.2%), cooked food (40.8%), cooked poultry meat (32.7%), seafood products (32.3%), spices (28.8%), canned products (16.7%), raw poultry meat (9.4%), fresh-cut vegetables (5.0%), and dairy products (4.8%). The 174 B. cereus isolates were characterized by partial sequencing of the panC gene, using a Sym'Previous software tool to assign them to different phylogenetic groups. Strains were distributed as follows: 61.3, 29.5, 7.5, and 1.7% in the group III, IV, II, and V, respectively. The genetic diversity was further assessed by ERIC-PCR and PFGE

Isolation, Identification, Prevalence, and Genetic Diversity of Bacillus cereus Group Bacteria From Different Foodstuffs in Tunisia

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Maroua Gdoura-Ben Amor

2018-03-01

Full Text Available Bacillus cereus group is widespread in nature and foods. Several members of this group are recognized as causing food spoilage and/or health issues. This study was designed to determine the prevalence and genetic diversity of the B. cereus group strains isolated in Tunisia from different foods (cereals, spices, cooked food, fresh-cut vegetables, raw and cooked poultry meats, seafood, canned, pastry, and dairy products. In total, 687 different samples were collected and searched for the presence of the B. cereus group after selective plating on MYP agar and enumeration of each sample. The typical pink-orange uniform colonies surrounded by a zone of precipitate were assumed to belong to the B. cereus group. One typical colony from each sample was subcultured and preserved as cryoculture. Overall, 191 (27.8% food samples were found positive, giving rise to a collection of 191 B. cereus-like isolates. The concentration of B. cereus-like bacteria were below 103 cfu/g or ml in 77.5% of the tested samples. Higher counts (>104 cfu/g or ml were found in 6.8% of samples including fresh-cut vegetables, cooked foods, cereals, and pastry products. To verify whether B. cereus-like isolates belonged to the B. cereus group, a PCR test targeting the sspE gene sequence specific of the group was carried out. Therefore, 174 isolates were found to be positive. Food samples were contaminated as follows: cereals (67.6%, pastry products (46.2%, cooked food (40.8%, cooked poultry meat (32.7%, seafood products (32.3%, spices (28.8%, canned products (16.7%, raw poultry meat (9.4%, fresh-cut vegetables (5.0%, and dairy products (4.8%. The 174 B. cereus isolates were characterized by partial sequencing of the panC gene, using a Sym'Previous software tool to assign them to different phylogenetic groups. Strains were distributed as follows: 61.3, 29.5, 7.5, and 1.7% in the group III, IV, II, and V, respectively. The genetic diversity was further assessed by ERIC-PCR and PFGE

Ampicillin-Resistant Non-β-Lactamase-Producing Haemophilus influenzae in Spain: Recent Emergence of Clonal Isolates with Increased Resistance to Cefotaxime and Cefixime▿

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García-Cobos, Silvia; Campos, José; Lázaro, Edurne; Román, Federico; Cercenado, Emilia; García-Rey, César; Pérez-Vázquez, María; Oteo, Jesús; de Abajo, Francisco

2007-01-01

The sequence of the ftsI gene encoding the transpeptidase domain of penicillin-binding protein 3 (PBP 3) was determined for 354 nonconsecutive Haemophilus influenzae isolates from Spain; 17.8% of them were ampicillin susceptible, 56% were β-lactamase nonproducing ampicillin resistant (BLNAR), 15.8% were β-lactamase producers and ampicillin resistant, and 10.4% displayed both resistance mechanisms. The ftsI gene sequences had 28 different mutation patterns and amino acid substitutions at 23 positions. Some 93.2% of the BLNAR strains had amino acid substitutions at the Lys-Thr-Gly (KTG) motif, the two most common being Asn526 to Lys (83.9%) and Arg517 to His (9.3%). Amino acid substitutions at positions 377, 385, and 389, which conferred cefotaxime and cefixime MICs 10 to 60 times higher than those of susceptible strains, were found for the first time in Europe. In 72 isolates for which the repressor acrR gene of the AcrAB efflux pump was sequenced, numerous amino acid substitutions were found. Eight isolates with ampicillin MICs of 0.25 to 2 μg/ml showed changes that predicted the early termination of the acrR reading frame. Pulsed-field gel electrophoresis analysis demonstrated that most BLNAR strains were genetically diverse, although clonal dissemination was detected in a group of isolates presenting with increased resistance to cefotaxime and cefixime. Background antibiotic use at the community level revealed a marked trend toward increased amoxicillin-clavulanic acid consumption. BLNAR H. influenzae strains have arisen by vertical and horizontal spread and have evolved to adapt rapidly to the increased selective pressures posed by the use of oral penicillins and cephalosporins. PMID:17470649

Low level of sequence diversity at merozoite surface protein-1 locus of Plasmodium ovale curtisi and P. ovale wallikeri from Thai isolates.

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Putaporntip, Chaturong; Hughes, Austin L; Jongwutiwes, Somchai

2013-01-01

The merozoite surface protein-1 (MSP-1) is a candidate target for the development of blood stage vaccines against malaria. Polymorphism in MSP-1 can be useful as a genetic marker for strain differentiation in malarial parasites. Although sequence diversity in the MSP-1 locus has been extensively analyzed in field isolates of Plasmodium falciparum and P. vivax, the extent of variation in its homologues in P. ovale curtisi and P. ovale wallikeri, remains unknown. Analysis of the mitochondrial cytochrome b sequences of 10 P. ovale isolates from symptomatic malaria patients from diverse endemic areas of Thailand revealed co-existence of P. ovale curtisi (n = 5) and P. ovale wallikeri (n = 5). Direct sequencing of the PCR-amplified products encompassing the entire coding region of MSP-1 of P. ovale curtisi (PocMSP-1) and P. ovale wallikeri (PowMSP-1) has identified 3 imperfect repeated segments in the former and one in the latter. Most amino acid differences between these proteins were located in the interspecies variable domains of malarial MSP-1. Synonymous nucleotide diversity (πS) exceeded nonsynonymous nucleotide diversity (πN) for both PocMSP-1 and PowMSP-1, albeit at a non-significant level. However, when MSP-1 of both these species was considered together, πS was significantly greater than πN (pdiversity at this locus prior to speciation. Phylogenetic analysis based on conserved domains has placed PocMSP-1 and PowMSP-1 in a distinct bifurcating branch that probably diverged from each other around 4.5 million years ago. The MSP-1 sequences support that P. ovale curtisi and P. ovale wallikeri are distinct species. Both species are sympatric in Thailand. The low level of sequence diversity in PocMSP-1 and PowMSP-1 among Thai isolates could stem from persistent low prevalence of these species, limiting the chance of outcrossing at this locus.

Molecular Epidemiology Reveals Genetic Diversity amongst Isolates of the Cryptococcus neoformans/C. gattii Species Complex in Thailand

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Kaocharoen, Sirada; Ngamskulrungroj, Popchai; Firacative, Carolina; Trilles, Luciana; Piyabongkarn, Dumrongdej; Banlunara, Wijit; Poonwan, Natteewan; Chaiprasert, Angkana; Meyer, Wieland; Chindamporn, Ariya

2013-01-01

To gain a more detailed picture of cryptococcosis in Thailand, a retrospective study of 498 C. neoformans and C. gattii isolates has been conducted. Among these, 386, 83 and 29 strains were from clinical, environmental and veterinary sources, respectively. A total of 485 C. neoformans and 13 C. gattii strains were studied. The majority of the strains (68.9%) were isolated from males (mean age of 37.97 years), 88.5% of C. neoformans and only 37.5% of C. gattii strains were from HIV patients. URA5-RFLP and/or M13 PCR-fingerprinting analysis revealed that the majority of the isolates were C. neoformans molecular type VNI regardless of their sources (94.8%; 94.6% of the clinical, 98.8% of the environmental and 86.2% of the veterinary isolates). In addition, the molecular types VNII (2.4%; 66.7% of the clinical and 33.3% of the veterinary isolates), VNIV (0.2%; 100% environmental isolate), VGI (0.2%; 100% clinical isolate) and VGII (2.4%; 100% clinical isolates) were found less frequently. Multilocus Sequence Type (MLST) analysis using the ISHAM consensus MLST scheme for the C. neoformans/C. gattii species complex identified a total of 20 sequence types (ST) in Thailand combining current and previous data. The Thai isolates are an integrated part of the global cryptococcal population genetic structure, with ST30 for C. gattii and ST82, ST83, ST137, ST141, ST172 and ST173 for C. neoformans being unique to Thailand. Most of the C. gattii isolates were ST7 = VGIIb, which is identical to the less virulent minor Vancouver island outbreak genotype, indicating Thailand as a stepping stone in the global spread of this outbreak strain. The current study revealed a greater genetic diversity and a wider range of major molecular types being present amongst Thai cryptococcal isolates than previously reported. PMID:23861989

Characterization of a Bacillus thuringiensis strain collection isolated from diverse Costa Rican natural ecosystems

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Glen Arrieta

2006-03-01

Full Text Available Costa Rican natural ecosystems are among the most diverse in the world. For this reason, we isolated strains of the entomopathogenic bacteria Bacillus thuringiensis (Bt to determine their diversity, distribution and abundance. A total of 146 Bt strains were obtained from environmental samples collected from diverse natural ecosystems and life zones of Costa Rica. We recovered Bt strains from 71%, 63%, 61% and 54% of soil samples, fresh leaves, other substrates and leaf litter respectively. Bt was isolated in 65%of the samples collected in the humid tropical forest in national parks (Braulio Carrillo, Gandoca Manzanillo, Sierpe, Hitoy Cerere, and Cahuita, and in 59% of the samples collected in the dry tropical forest (Parque Nacional Marino las Baulas, Palo Verde and Santa Rosa. In the very humid tropical forest (Tortuguero Bt was isolated in 75% of the samples and in the very humid tropical forest transition perhumid (Cararait was found in 69% of the samples. The strains exhibit a diverse number, size and morphology of parasporal inclusion bodies: irregular (47%,oval (20%, bipyramidal (3%, bipyramidal and cubic (1%, bipyramidal, oval and irregular (5% and bipyramidal, oval and cubic crystals (2%. Strains isolated from Braulio Carrillo, Tortuguero and Cahuita, presented predominantly irregular crystals. On the other hand, more than 60% of the isolates from Térraba-Sierpe and Hitoy-Cerere had medium oval crystals. Strains from Gandoca-Manzanillo, Palo Verde and Carara presented mainly combinations of oval and irregular crystals. Nevertheless, the greatest diversity in crystal morphology was observed in those from Santa Rosa, Llanos del Río Medio Queso and Parque Marino las Baulas. Protein analyses of the crystal-spore preparations showed ä -endotoxin with diverse electrophoretic patterns, with molecular weights in the range of 20 to 160 kDa. Fifty six percent of the strains amplified with the cry2 primer, 54% with vip3, 20% with cry1, 9% with

Y-chromosomal diversity of the Valachs from the Czech Republic: model for isolated population in Central Europe

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Ehler, Edvard; Vaněk, Daniel; Stenzl, Vlastimil; Vančata, Václav

2011-01-01

Aim To evaluate Y-chromosomal diversity of the Moravian Valachs of the Czech Republic and compare them with a Czech population sample and other samples from Central and South-Eastern Europe, and to evaluate the effects of genetic isolation and sampling. Methods The first sample set of the Valachs consisted of 94 unrelated male donors from the Valach region in northeastern Czech Republic border-area. The second sample set of the Valachs consisted of 79 men who originated from 7 paternal lineages defined by surname. No close relatives were sampled. The third sample set consisted of 273 unrelated men from the whole of the Czech Republic and was used for comparison, as well as published data for other 27 populations. The total number of samples was 3244. Y-short tandem repeat (STR) markers were typed by standard methods using PowerPlex® Y System (Promega) and Yfiler® Amplification Kit (Applied Biosystems) kits. Y-chromosomal haplogroups were estimated from the haplotype information. Haplotype diversity and other intra- and inter-population statistics were computed. Results The Moravian Valachs showed a lower genetic variability of Y-STR markers than other Central European populations, resembling more to the isolated Balkan populations (Aromuns, Csango, Bulgarian, and Macedonian Roma) than the surrounding populations (Czechs, Slovaks, Poles, Saxons). We illustrated the effect of sampling on Valach paternal lineages, which includes reduction of discrimination capacity and variability inside Y-chromosomal haplogroups. Valach modal haplotype belongs to R1a haplogroup and it was not detected in the Czech population. Conclusion The Moravian Valachs display strong substructure and isolation in their Y chromosomal markers. They represent a unique Central European population model for population genetics. PMID:21674832

Diversity and Symbiotic Characteristics of Cowpea Bradyrhizobium Strains in Ghanaian Soils

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Fening, Joseph Opoku

1999-08-01

This study reports investigation of the biodiversity of bradyrhizobia isolates that nodulate cowpea in Ghanaian soils. As a prelude, some components of nitrogen fixation of cowpea in the various soils were examined through: (1) assessment of the natural nodulation of 45 cowpea cultivars in 20 soils sampled from 5 ecozones (coastal savanna, tain forest, semi deciduous forest, forest savanna transition and guinea savanna), (2) determination of the numbers of bradyrhizobial isolates in the soils and (3) determination of the response of cowpea to nitrogen fertilization. The results of the ability of 45 cowpea cultivars to nodulate naturally in different soil types showed large variability among the cultivars. Counts of the indigenous bradyrhizobia population in the soils showed that most of the soils in Ghana harbour large populations of bradyrhizobia (in the range of 0.6 x 10 to 31 x 10 3 ) capable of nodulating cowpea. Response of cowpea to nitrogen fertilizer differed in the different soils. In general all the cultivars showed significant responses to increasing levels of nitrogen, an indication that nitrogen fixation was not supplying the plants with all the external nitrogen required for maximum yield. A combination of morpho-physiological and molecular analysis was used to assess the diversity of the bradyrhizobia isolates. A total of 100 isolates were assessed. The results of the morpho physiological analysis indicated that cowpea is nodulated by both fast and slow growing rhizobia. The results also showed that the isolates were versatile and could survive under different soil conditions particularly acidity and salt stress. A cross inoculation study of the isolates with nine legume species produced seven major groupings with 28 subgroups based on distinct nodulation patterns. Results of the serology (ELISA) assay indicated that only a small fraction of the isolates reacted strongly with antisera of each other. The greater proportion showed no cross reactivity

Cyanobacterial diversity and halotolerance in a variable hypersaline environment.

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Kirkwood, Andrea E; Buchheim, Julie A; Buchheim, Mark A; Henley, William J

2008-04-01

The Great Salt Plains (GSP) in north-central Oklahoma, USA is an expansive salt flat (approximately 65 km(2)) that is part of the federally protected Salt Plains National Wildlife Refuge. The GSP serves as an ideal environment to study the microbial diversity of a terrestrial, hypersaline system that experiences wide fluctuations in freshwater influx and diel temperature. Our study assessed cyanobacterial diversity at the GSP by focusing on the taxonomic and physiological diversity of GSP isolates, and the 16S rRNA phylogenetic diversity of isolates and environmental clones from three sites (north, central, and south). Taxonomic diversity of isolates was limited to a few genera (mostly Phormidium and Geitlerinema), but physiological diversity based on halotolerance ranges was strikingly more diverse, even between strains of the same phylotype. The phylogenetic tree revealed diversity that spanned a number of cyanobacterial lineages, although diversity at each site was dominated by only a few phylotypes. Unlike other hypersaline systems, a number of environmental clones from the GSP were members of the heterocystous lineage. Although a number of cyanobacterial isolates were close matches with prevalent environmental clones, it is not certain if these clones reflect the same halotolerance ranges of their matching isolates. This caveat is based on the notable disparities we found between strains of the same phylotype and their inherent halotolerance. Our findings support the hypothesis that variable or poikilotrophic environments promote diversification, and in particular, select for variation in ecotype more than phylotype.

Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating rural-urban habitats.

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Wereszczuk, Anna; Leblois, Raphaël; Zalewski, Andrzej

2017-12-22

Population genetic diversity and structure are determined by past and current evolutionary processes, among which spatially limited dispersal, genetic drift, and shifts in species distribution boundaries have major effects. In most wildlife species, environmental modifications by humans often lead to contraction of species' ranges and/or limit their dispersal by acting as environmental barriers. However, in species well adapted to anthropogenic habitat or open landscapes, human induced environmental changes may facilitate dispersal and range expansions. In this study, we analysed whether isolation by distance and deforestation, among other environmental features, promotes or restricts dispersal and expansion in stone marten (Martes foina) populations. We genotyped 298 martens from eight sites at twenty-two microsatellite loci to characterize the genetic variability, population structure and demographic history of stone martens in Poland. At the landscape scale, limited genetic differentiation between sites in a mosaic of urban, rural and forest habitats was mostly influenced by isolation by distance. Statistical clustering and multivariate analyses showed weak genetic structuring with two to four clusters and a high rate of gene flow between them. Stronger genetic differentiation was detected for one stone marten population (NE1) located inside a large forest complex. Genetic differentiation between this site and all others was 20% higher than between other sites separated by similar distances. The genetic uniqueness index of NE1 was also twofold higher than in other sites. Past demographic history analyses showed recent expansion of this species in north-eastern Poland. A decrease in genetic diversity from south to north, and MIGRAINE analyses indicated the direction of expansion of stone marten. Our results showed that two processes, changes in species distribution boundaries and limited dispersal associated with landscape barriers, affect genetic diversity and

Prevalence and diversity of Escherichia coli isolated from a barley trial supplemented with bulky organic soil amendments: green compost and bovine slurry.

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Holden, N J; Wright, F; Mackenzie, K; Marshall, J; Mitchell, S; Mahajan, A; Wheatley, R; Daniell, T J

2014-03-01

A barley field trial supplemented with bulky organic soil amendments, municipal compost or bovine slurry was sampled for Escherichia coli to test the hypothesis that E. coli isolated from the soil or from barley plants were derived from bovine slurry. A qualitative analysis showed that a total of 12% of the bulk soil cores and 16% of harvested grain samples yielded E. coli. The strongest association for positive detection of E. coli from soil was with time of year and for slurry-treated plots, with irrigation. However, E. coli were detected in plots from all treatment types and not exclusively associated with bovine slurry. Phylogroup, plasmid profiling and population genetics analysis (multilocus sequence typing) revealed extensive genetic diversity. Identical sequence types for slurry and soil isolates were detected, indicative of direct transfer into the soil, although not frequently. Host interaction assays with selected isolates showed a variation in the ability to colonize barley roots, but not in interactions with bovine cells. The work has implications in appropriate use of E. coli as a faecal indicator as isolates were widespread and diverse, reinforcing the view that some are a natural part of the microflora in agricultural systems. Faecal deposition is considered to be the main process that introduces Escherichia coli into soil, giving rise to their use as a faecal indication species and the potential for cycling pathogens in agricultural systems. We found that bovine slurry was not the main source of E. coli in a barley trial and a high degree of diversity was present in the collection. The findings support the hypothesis that the population structure of E. coli in secondary habitats is shaped by the environment and highlight the drawbacks of its use as a faecal indicator species. © 2013 The Society for Applied Microbiology.

Genetic Diversity of Nitrogen-Fixing and Plant Growth Promoting Pseudomonas Species Isolated from Sugarcane Rhizosphere.

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Li, Hai-Bi; Singh, Rajesh K; Singh, Pratiksha; Song, Qi-Qi; Xing, Yong-Xiu; Yang, Li-Tao; Li, Yang-Rui

2017-01-01

The study was designed to isolate and characterize Pseudomonas spp. from sugarcane rhizosphere, and to evaluate their plant- growth- promoting (PGP) traits and nitrogenase activity. A biological nitrogen-fixing microbe has great potential to replace chemical fertilizers and be used as a targeted biofertilizer in a plant. A total of 100 isolates from sugarcane rhizosphere, belonging to different species, were isolated; from these, 30 isolates were selected on the basis of preliminary screening, for in vitro antagonistic activities against sugarcane pathogens and for various PGP traits, as well as nitrogenase activity. The production of IAA varied from 312.07 to 13.12 μg mL -1 in tryptophan supplemented medium, with higher production in AN15 and lower in CN20 strain. The estimation of ACC deaminase activity, strains CY4 and BA2 produced maximum and minimum activity of 77.0 and 15.13 μmoL mg -1 h -1 . For nitrogenase activity among the studied strains, CoA6 fixed higher and AY1 fixed lower in amounts (108.30 and 6.16 μmoL C 2 H 2 h -1 mL -1 ). All the strains were identified on the basis of 16S rRNA gene sequencing, and the phylogenetic diversity of the strains was analyzed. The results identified all strains as being similar to Pseudomonas spp. Polymerase chain reaction (PCR) amplification of nifH and antibiotic genes was suggestive that the amplified strains had the capability to fix nitrogen and possessed biocontrol activities. Genotypic comparisons of the strains were determined by BOX, ERIC, and REP PCR profile analysis. Out of all the screened isolates, CY4 ( Pseudomonas koreensis ) and CN11 ( Pseudomonas entomophila ) showed the most prominent PGP traits, as well as nitrogenase activity. Therefore, only these two strains were selected for further studies; Biolog profiling; colonization through green fluorescent protein (GFP)-tagged bacteria; and nifH gene expression using quantitative real-time polymerase chain reaction (qRT-PCR) analysis. The Biolog

Genetic diversity, anti-microbial resistance, plasmid profile and frequency of the Vi antigen in Salmonella Dublin strains isolated in Brazil.

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Vilela, F P; Frazão, M R; Rodrigues, D P; Costa, R G; Casas, M R T; Fernandes, S A; Falcão, J P; Campioni, F

2018-02-01

Salmonella Dublin is strongly adapted to cattle causing enteritis and/or systemic disease with high rates of mortality. However, it can be sporadically isolated from humans, usually causing serious disease, especially in patients with underlying chronic diseases. The aim of this study was to molecularly type S. Dublin strains isolated from humans and animals in Brazil to verify the diversity of these strains as well as to ascertain possible differences between strains isolated from humans and animals. Moreover, the presence of the capsular antigen Vi and the plasmid profile was characterized in addition to the anti-microbial resistance against 15 drugs. For this reason, 113 S. Dublin strains isolated between 1983 and 2016 from humans (83) and animals (30) in Brazil were typed by PFGE and MLVA. The presence of the capsular antigen Vi was verified by PCR, and the phenotypic expression of the capsular antigen was determined serologically. Also, a plasmid analysis for each strain was carried out. The strains studied were divided into 35 different PFGE types and 89 MLVA-types with a similarity of ≥80% and ≥17.5%, respectively. The plasmid sizes found ranged from 2 to >150 kb and none of the strains studied presented the capsular antigen Vi. Resistance or intermediate resistance was found in 23 strains (20.3%) that were resistant to ampicillin, ciprofloxacin, chloramphenicol, imipenem, nalidixic acid, piperacillin, streptomycin and/or tetracycline. The majority of the S. Dublin strains studied and isolated over a 33-year period may descend from a common subtype that has been contaminating humans and animals in Brazil and able to cause invasive disease even in the absence of the capsular antigen. The higher diversity of resistance phenotypes in human isolates, as compared with animal strains, may be a reflection of the different anti-microbial treatments used to control S. Dublin infections in humans in Brazil. © 2017 Blackwell Verlag GmbH.

Genetic diversity of Haemonchus contortus isolated from sympatric wild blue sheep (Pseudois nayaur) and sheep in Helan Mountains, China.

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Shen, Dong-Dong; Wang, Ji-Fei; Zhang, Dan-Yu; Peng, Zhi-Wei; Yang, Tian-Yun; Wang, Zhao-Ding; Bowman, Dwight D; Hou, Zhi-Jun; Liu, Zhen-Sheng

2017-09-19

Haemonchus contortus is known among parasitic nematodes as one of the major veterinary pathogens of small ruminants and results in great economic losses worldwide. Human activities, such as the sympatric grazing of wild with domestic animals, may place susceptible wildlife hosts at risk of increased prevalence and infection intensity with this common small ruminant parasite. Studies on phylogenetic factors of H. contortus should assist in defining the amount of the impact of anthropogenic factors on the extent of sharing of agents such as this nematode between domestic animals and wildlife. H. contortus specimens (n = 57) were isolated from wild blue sheep (Pseudois nayaur) inhabiting Helan Mountains (HM), China and additional H. contortus specimens (n = 20) were isolated from domestic sheep that were grazed near the natural habitat of the blue sheep. Complete ITS2 (second internal transcribed spacer) sequences and partial sequences of the nad4 (nicotinamide dehydrogenase subunit 4 gene) gene were amplified to determine the sequence variations and population genetic diversities between these two populations. Also, 142 nad4 haplotype sequences of H. contortus from seven other geographical regions of China were retrieved from database to further examine the H. contortus population structure. Sequence analysis revealed 10 genotypes (ITS2) and 73 haplotypes (nad4) among the 77 specimens, with nucleotide diversities of 0.007 and 0.021, respectively, similar to previous studies in other countries, such as Pakistan, Malaysia and Yemen. Phylogenetic analyses (BI, MP, NJ) of nad4 sequences showed that there were no noticeable boundaries among H. contortus populations from different geographical origin and population genetic analyses revealed that most of the variation (94.21%) occurred within H. contortus populations. All phylogenetic analyses indicated that there was little genetic differentiation but a high degree of gene flow among the H. contortus populations among

Changes of Bacterial Diversity Depend on the Spoilage of Fresh Vegetables

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Dong Hwan Lee

2011-04-01

Full Text Available Almost 10~30% of vegetables were discarded by the spoilage from farms to tables. After harvest, vegetables are often spoiled by a wide variety of microorganisms including many bacterial and fungal species. This investigation was conducted to extent the knowledge of relationship the spoilage of vegetables and the diversity of microbes. The total aerobic bacterial numbers in fresh lettuce, perilla leaf, and chicory were 2.6~2.7×106, 4.6×105, 1.2×106 CFU/g of fresh weight, respectively. The most common bacterial species were Pseudomonas spp., Alysiella spp., and Burkholderia spp., and other 18 more genera were involved in. After one week of incubation of those vegetables at 28℃, the microbial diversity had been changed. The total aerobic bacterial numbers increased to 1.1~4.6×108, 4.9×107, and 7.6×108 CFU/g of fresh weight for lettuce, perilla leaf, and chicory that is about 102 times increased bacterial numbers than that before spoilage. However, the diversity of microbes isolated had been simplified and fewer bacterial species had been isolated. The most bacterial population (~48% was taken up by Pseudomonas spp., and followed by Arthrobacter spp. and Bacillus spp. The spoilage activity of individual bacterial isolates had been tested using axenic lettuce plants. Among tested isolates, Pseudomonas fluorescence and Pantoea agglomerans caused severe spoilage on lettuce.

Genetic diversity of NS3 protease from Brazilian HCV isolates and possible implications for therapy with direct-acting antiviral drugs

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Allan Peres-da-Silva

2012-03-01

Full Text Available The hepatitis C virus (HCV NS3 protease has been one of the molecular targets of new therapeutic approaches. Its genomic sequence variability in Brazilian HCV isolates is poorly documented. To obtain more information on the magnitude of its genetic diversity, 114 Brazilian HCV samples were sequenced and analysed together with global reference sequences. Genetic distance (d analyses revealed that subtype 1b had a higher degree of heterogeneity (d = 0.098 than subtypes 1a (d = 0.060 and 3a (d = 0.062. Brazilian isolates of subtype 1b were distributed in the phylogenetic tree among sequences from other countries, whereas most subtype 1a and 3a sequences clustered into a single branch. Additional characterisation of subtype 1a in clades 1 and 2 revealed that all but two Brazilian subtype 1a sequences formed a distinct and strongly supported (approximate likelihood-ratio test = 93 group of sequences inside clade 1. Moreover, this subcluster inside clade 1 presented an unusual phenotypic characteristic in relation to the presence of resistance mutations for macrocyclic inhibitors. In particular, the mutation Q80K was found in the majority of clade 1 sequences, but not in the Brazilian isolates. These data demonstrate that Brazilian HCV subtypes display a distinct pattern of genetic diversity and reinforce the importance of sequence information in future therapeutic approaches.

Tourism in Antarctica : Increasing Diversity and the Legal Criteria for Authorisation

NARCIS (Netherlands)

Bastmeijer, C.J.

2003-01-01

Both the intensity and the diversity of tourist activities in Antarctica are increasing. Activities conducted in the Antarctic today include ski-expeditions, mountain climbing, marathons, long-distance swimming and scuba diving. In this article the question is discussed whether the Protocol on

Genetic diversity in the C-terminus of merozoite surface protein 1 among Plasmodium knowlesi isolates from Selangor and Sabah Borneo, Malaysia.

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Yap, Nan Jiun; Goh, Xiang Ting; Koehler, Anson V; William, Timothy; Yeo, Tsin Wen; Vythilingam, Indra; Gasser, Robin B; Lim, Yvonne A L

2017-10-01

Plasmodium knowlesi, a malaria parasite of macaques, has emerged as an important parasite of humans. Despite the significance of P. knowlesi malaria in parts of Southeast Asia, very little is known about the genetic variation in this parasite. Our aim here was to explore sequence variation in a molecule called the 42kDa merozoite surface protein-1 (MSP-1), which is found on the surface of blood stages of Plasmodium spp. and plays a key role in erythrocyte invasion. Several studies of P. falciparum have reported that the C-terminus (a 42kDa fragment) of merozoite surface protein-1 (MSP-1 42 ; consisting of MSP-1 19 and MSP-1 33 ) is a potential candidate for a malaria vaccine. However, to date, no study has yet investigated the sequence diversity of the gene encoding P. knowlesi MSP-1 42 (comprising Pk-msp-1 19 and Pk-msp-1 33 ) among isolates in Malaysia. The present study explored this aspect. Twelve P. knowlesi isolates were collected from patients from hospitals in Selangor and Sabah Borneo, Malaysia, between 2012 and 2014. The Pk-msp-1 42 gene was amplified by PCR and directly sequenced. Haplotype diversity (Hd) and nucleotide diversity (л) were studied among the isolates. There was relatively high genetic variation among P. knowlesi isolates; overall Hd and л were 1±0.034 and 0.01132±0.00124, respectively. A total of nine different haplotypes related to amino acid alterations at 13 positions, and the Pk-MSP-1 19 sequence was found to be more conserved than Pk-msp-1 33 . We have found evidence for negative selection in Pk-msp- 42 as well as the 33kDa and 19kDa fragments by comparing the rate of non-synonymous versus synonymous substitutions. Future investigations should study large numbers of samples from disparate geographical locations to critically assess whether this molecule might be a potential vaccine target for P. knowlesi. Copyright © 2017 Elsevier B.V. All rights reserved.

The relationship between cultural competence education and increasing diversity in nursing schools and practice settings.

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Pacquiao, Dula

2007-01-01

This article attempted to examine the relationship between cultural competence education and increasing diversity in nursing schools and practice settings. In addition to the review of the literature, a panel of experts was interviewed regarding institutional practices in response to the challenge of increasing diversity and cultural competence education. Evidence of positive outcomes of cultural competent care and impact of race and ethnic concordance between patients and providers are presented. The challenge of increasing underrepresented minorities in health care professions remains elusive. An ecological analysis is recommended to address the social and cultural barriers that transcend the micro system of the school and the macro system of the society. The challenge of increasing diversity and realizing outcomes of cultural competence education requires social and comprehensive remedies to level life inequities that perpetuate a history of disadvantages in some groups.

American Society of Clinical Oncology Strategic Plan for Increasing Racial and Ethnic Diversity in the Oncology Workforce.

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Winkfield, Karen M; Flowers, Christopher R; Patel, Jyoti D; Rodriguez, Gladys; Robinson, Patricia; Agarwal, Amit; Pierce, Lori; Brawley, Otis W; Mitchell, Edith P; Head-Smith, Kimberly T; Wollins, Dana S; Hayes, Daniel F

2017-08-01

In December 2016, the American Society of Clinical Oncology (ASCO) Board of Directors approved the ASCO Strategic Plan to Increase Racial and Ethnic Diversity in the Oncology Workforce. Developed through a multistakeholder effort led by the ASCO Health Disparities Committee, the purpose of the plan is to guide the formal efforts of ASCO in this area over the next three years (2017 to 2020). There are three primary goals: (1) to establish a longitudinal pathway for increasing workforce diversity, (2) to enhance ASCO leadership diversity, and (3) to integrate a focus on diversity across ASCO programs and policies. Improving quality cancer care in the United States requires the recruitment of oncology professionals from diverse backgrounds. The ASCO Strategic Plan to Increase Racial and Ethnic Diversity in the Oncology Workforce is designed to enhance existing programs and create new opportunities that will move us closer to the vision of achieving an oncology workforce that reflects the demographics of the US population it serves.

Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain.

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Shen, Congcong; Shi, Yu; Ni, Yingying; Deng, Ye; Van Nostrand, Joy D; He, Zhili; Zhou, Jizhong; Chu, Haiyan

2016-01-01

The elevational and latitudinal diversity patterns of microbial taxa have attracted great attention in the past decade. Recently, the distribution of functional attributes has been in the spotlight. Here, we report a study profiling soil microbial communities along an elevation gradient (500-2200 m) on Changbai Mountain. Using a comprehensive functional gene microarray (GeoChip 5.0), we found that microbial functional gene richness exhibited a dramatic increase at the treeline ecotone, but the bacterial taxonomic and phylogenetic diversity based on 16S rRNA gene sequencing did not exhibit such a similar trend. However, the β-diversity (compositional dissimilarity among sites) pattern for both bacterial taxa and functional genes was similar, showing significant elevational distance-decay patterns which presented increased dissimilarity with elevation. The bacterial taxonomic diversity/structure was strongly influenced by soil pH, while the functional gene diversity/structure was significantly correlated with soil dissolved organic carbon (DOC). This finding highlights that soil DOC may be a good predictor in determining the elevational distribution of microbial functional genes. The finding of significant shifts in functional gene diversity at the treeline ecotone could also provide valuable information for predicting the responses of microbial functions to climate change.

Molecular epidemiology of Corynebacterium pseudotuberculosis isolated from horses in California.

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Haas, Dionei J; Dorneles, Elaine M S; Spier, Sharon J; Carroll, Scott P; Edman, Judy; Azevedo, Vasco A; Heinemann, Marcos B; Lage, Andrey P

2017-04-01

Corynebacterium pseudotuberculosis biovar Equi is an important pathogen of horses. It is increasing in frequency in the United States, and is responsible for various clinical forms of infection, including external abscesses, internal abscesses of the abdominal or thoracic cavities, and ulcerative lymphangitis. The host/pathogen factors dictating the form or severity of infection are currently unknown. Our recent investigations have shown that genotyping C. pseudotuberculosis isolates using enterobacterial repetitive intergenic consensus (ERIC)-PCR is useful for understanding the evolutionary genetics of the species as well for molecular epidemiology studies. The aims of the present study were to assess (i) the genetic diversity of C. pseudotuberculosis strains isolated from horses in California, United States and (ii) the epidemiologic relationships among isolates. One hundred and seven C. pseudotuberculosis biovar Equi isolates from ninety-five horses, and two C. pseudotuberculosis biovar Ovis strains, C. pseudotuberculosis ATCC 19410 T type strain and C. pseudotuberculosis 1002 vaccine strain, were fingerprinted using the ERIC 1+2-PCR. C. pseudotuberculosis isolated from horses showed a high genetic diversity, clustering in twenty-seven genotypes with a diversity index of 0.91. Minimal spanning tree showed four major clonal complexes with a pattern of temporal clustering. Strains isolated from the same horse showed identical ERIC 1+2-PCR genotype, with the exception of two strains isolated from the same animal that showed distinct genotypes, suggesting a co-infection. We found no strong genetic signals related to clinical form (including internal versus external infections). However, temporal clustering of genotypes was observed. Copyright © 2016. Published by Elsevier B.V.

Three distinct clones of carbapenem-resistant Acinetobacter baumannii with high diversity of carbapenemases isolated from patients in two hospitals in Kuwait

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N.A. Al-Sweih

2012-02-01

Full Text Available Summary: Objectives: This study was undertaken to investigate the clonal relatedness of multidrug-resistant (MDR Acinetobacter baumannii isolates collected from patients in two teaching hospitals in Kuwait. Materials and methods: Clinically significant consecutive isolates of A. baumannii obtained from patients in the Mubarak (36 and Adan (58 hospitals over a period of 6 months were studied. These isolates were identified using molecular methods, and their antimicrobial susceptibility was determined by the Etest method. The mechanism of resistance to carbapenem was investigated by PCR, and pulsed-field gel electrophoresis (PFGE was used to determine the clonal relatedness of MDR isolates. Results: Of the 94 isolates investigated, 80 (85.1% were multidrug resistant (MDR. The A. baumannii PFGE clone A and subclone A1 were the most prevalent in patients infected with MDR isolates. Fifty-five (94.8% and 15 (41.7% of the MDR isolates from the Adan and Mubarak hospitals, respectively, belonged to PFGE clone A; isolates in this group showed higher resistance rates to antibiotics than isolates form other groups. Of the 94 isolates, 40 (42.6% were resistant to either imipenem or meropenem or to both (CRAB. Most CRAB isolates (29/40 or 72.5% carried bla genes, which code for MBL (VIM-2 and IMP-1 enzymes. Two isolates harbored blaOXA-23. Conclusion: Three distinct clones of CRAB were isolated, providing evidence of a high diversity of carbapenemases among our geographically related isolates. Keywords: MDR A. baumannii, Genotypes, bla genes, Kuwait hospitals

Ecological prevalence, genetic diversity and epidemiological aspects of Salmonella isolated from tomato agricultural regions of the Virginia Eastern Shore

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Rebecca L. Bell

2015-05-01

Full Text Available Virginia is the third largest producer of fresh-market tomatoes in the United States. Tomatoes grown along the eastern shore of Virginia are implicated almost yearly in Salmonella illnesses. Traceback implicates contamination occurring in the pre-harvest environment. To get a better understanding of the ecological niches of Salmonella in the tomato agricultural environment, a two-year study was undertaken at a regional agricultural research farm in Virginia. Environmental samples, including tomato (fruit, blossoms and leaves, irrigation water, surface water and sediment, were collected over the growing season. These samples were analyzed for the presence of Salmonella using modified FDA-BAM methods. Molecular assays were used to screen the samples. Over 1500 samples were tested. Seventy-five samples tested positive for Salmonella yielding over 230 isolates. The most commonly isolated serovars were S. Newport and S. Javiana with pulsed-field gel electrophoresis yielding 39 different patterns. Genetic diversity was further underscored among many other serotypes, which showed multiple PFGE subtypes. Whole genome sequencing of several S. Newport isolates collected in 2010 compared to clinical isolates associated with tomato consumption showed very few single nucleotide differences between environmental isolates and clinical isolates suggesting a source link to Salmonella contaminated tomatoes. Nearly all isolates collected during two growing seasons of surveillance were obtained from surface water and sediment sources pointing to these sites as long-term reservoirs for persistent and endemic contamination of this environment.

Genetic analysis reveals diversity and genetic relationship among Trichoderma isolates from potting media, cultivated soil and uncultivated soil.

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Al-Sadi, Abdullah M; Al-Oweisi, Fatma A; Edwards, Simon G; Al-Nadabi, Hamed; Al-Fahdi, Ahmed M

2015-07-28

Trichoderma is one of the most common fungi in soil. However, little information is available concerning the diversity of Trichoderma in soil with no previous history of cultivation. This study was conducted to investigate the most common species and the level of genetic relatedness of Trichoderma species from uncultivated soil in relation to cultivated soil and potting media. A total of 24, 15 and 13 Trichoderma isolates were recovered from 84 potting media samples, 45 cultivated soil samples and 65 uncultivated soil samples, respectively. Analysis based on the internal transcribed spacer region of the ribosomal RNA (rRNA) and the translation elongation factor gene (EF1) indicated the presence of 9 Trichoderma species: T. harzianum (16 isolates), T. asperellum (13), T. citrinoviride (9), T. orientalis (3), T. ghanense (3), T. hamatum (3), T. longibrachiatum (2), T. atroviride (2), and T. viride (1). All species were found to occur in potting media samples, while five Trichoderma species were recovered from the cultivated soils and four from the uncultivated soils. AFLP analysis of the 52 Trichoderma isolates produced 52 genotypes and 993 polymorphic loci. Low to moderate levels of genetic diversity were found within populations of Trichoderma species (H = 0.0780 to 0.2208). Analysis of Molecular Variance indicated the presence of very low levels of genetic differentiation (Fst = 0.0002 to 0.0139) among populations of the same Trichoderma species obtained from the potting media, cultivated soil and uncultivated soil. The study provides evidence for occurrence of Trichoderma isolates in soil with no previous history of cultivation. The lack of genetic differentiation among Trichoderma populations from potting media, cultivated soil and uncultivated soil suggests that some factors could have been responsible for moving Trichoderma propagules among the three substrates. The study reports for the first time the presence of 4 Trichoderma species in Oman: T

Genomic Diversity of Lactobacillus salivarius▿ †

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Raftis, Emma J.; Salvetti, Elisa; Torriani, Sandra; Felis, Giovanna E.; O'Toole, Paul W.

2011-01-01

Strains of Lactobacillus salivarius are increasingly employed as probiotic agents for humans or animals. Despite the diversity of environmental sources from which they have been isolated, the genomic diversity of L. salivarius has been poorly characterized, and the implications of this diversity for strain selection have not been examined. To tackle this, we applied comparative genomic hybridization (CGH) and multilocus sequence typing (MLST) to 33 strains derived from humans, animals, or food. The CGH, based on total genome content, including small plasmids, identified 18 major regions of genomic variation, or hot spots for variation. Three major divisions were thus identified, with only a subset of the human isolates constituting an ecologically discernible group. Omission of the small plasmids from the CGH or analysis by MLST provided broadly concordant fine divisions and separated human-derived and animal-derived strains more clearly. The two gene clusters for exopolysaccharide (EPS) biosynthesis corresponded to regions of significant genomic diversity. The CGH-based groupings of these regions did not correlate with levels of production of bound or released EPS. Furthermore, EPS production was significantly modulated by available carbohydrate. In addition to proving difficult to predict from the gene content, EPS production levels correlated inversely with production of biofilms, a trait considered desirable in probiotic commensals. L. salivarius displays a high level of genomic diversity, and while selection of L. salivarius strains for probiotic use can be informed by CGH or MLST, it also requires pragmatic experimental validation of desired phenotypic traits. PMID:21131523

Unravelling the Molecular Epidemiology and Genetic Diversity among Burkholderia pseudomallei Isolates from South India Using Multi-Locus Sequence Typing.

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Tellapragada, Chaitanya; Kamthan, Aayushi; Shaw, Tushar; Ke, Vandana; Kumar, Subodh; Bhat, Vinod; Mukhopadhyay, Chiranjay

2016-01-01

There is a slow but steady rise in the case detection rates of melioidosis from various parts of the Indian sub-continent in the past two decades. However, the epidemiology of the disease in India and the surrounding South Asian countries remains far from well elucidated. Multi-locus sequence typing (MLST) is a useful epidemiological tool to study the genetic relatedness of bacterial isolates both with-in and across the countries. With this background, we studied the molecular epidemiology of 32 Burkholderia pseudomallei isolates (31 clinical and 1 soil isolate) obtained during 2006-2015 from various parts of south India using multi-locus sequencing typing and analysis. Of the 32 isolates included in the analysis, 30 (93.7%) had novel allelic profiles that were not reported previously. Sequence type (ST) 1368 (n = 15, 46.8%) with allelic profile (1, 4, 6, 4, 1, 1, 3) was the most common genotype observed. We did not observe a genotypic association of STs with geographical location, type of infection and year of isolation in the present study. Measure of genetic differentiation (FST) between Indian and the rest of world isolates was 0.14413. Occurrence of the same ST across three adjacent states of south India suggest the dispersion of B.pseudomallei across the south western coastal part of India with limited geographical clustering. However, majority of the STs reported from the present study remained as "outliers" on the eBURST "Population snapshot", suggesting the genetic diversity of Indian isolates from the Australasian and Southeast Asian isolates.

Unravelling the Molecular Epidemiology and Genetic Diversity among Burkholderia pseudomallei Isolates from South India Using Multi-Locus Sequence Typing.

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Chaitanya Tellapragada

Full Text Available There is a slow but steady rise in the case detection rates of melioidosis from various parts of the Indian sub-continent in the past two decades. However, the epidemiology of the disease in India and the surrounding South Asian countries remains far from well elucidated. Multi-locus sequence typing (MLST is a useful epidemiological tool to study the genetic relatedness of bacterial isolates both with-in and across the countries. With this background, we studied the molecular epidemiology of 32 Burkholderia pseudomallei isolates (31 clinical and 1 soil isolate obtained during 2006-2015 from various parts of south India using multi-locus sequencing typing and analysis. Of the 32 isolates included in the analysis, 30 (93.7% had novel allelic profiles that were not reported previously. Sequence type (ST 1368 (n = 15, 46.8% with allelic profile (1, 4, 6, 4, 1, 1, 3 was the most common genotype observed. We did not observe a genotypic association of STs with geographical location, type of infection and year of isolation in the present study. Measure of genetic differentiation (FST between Indian and the rest of world isolates was 0.14413. Occurrence of the same ST across three adjacent states of south India suggest the dispersion of B.pseudomallei across the south western coastal part of India with limited geographical clustering. However, majority of the STs reported from the present study remained as "outliers" on the eBURST "Population snapshot", suggesting the genetic diversity of Indian isolates from the Australasian and Southeast Asian isolates.

Diversity loss with persistent human disturbance increases vulnerability to ecosystem collapse.

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MacDougall, A S; McCann, K S; Gellner, G; Turkington, R

2013-02-07

Long-term and persistent human disturbances have simultaneously altered the stability and diversity of ecological systems, with disturbances directly reducing functional attributes such as invasion resistance, while eliminating the buffering effects of high species diversity. Theory predicts that this combination of environmental change and diversity loss increases the risk of abrupt and potentially irreversible ecosystem collapse, but long-term empirical evidence from natural systems is lacking. Here we demonstrate this relationship in a degraded but species-rich pyrogenic grassland in which the combined effects of fire suppression, invasion and trophic collapse have created a species-poor grassland that is highly productive, resilient to yearly climatic fluctuations, and resistant to invasion, but vulnerable to rapid collapse after the re-introduction of fire. We initially show how human disturbance has created a negative relationship between diversity and function, contrary to theoretical predictions. Fire prevention since the mid-nineteenth century is associated with the loss of plant species but it has stabilized high-yield annual production and invasion resistance, comparable to a managed high-yield low-diversity agricultural system. In managing for fire suppression, however, a hidden vulnerability to sudden environmental change emerges that is explained by the elimination of the buffering effects of high species diversity. With the re-introduction of fire, grasslands only persist in areas with remnant concentrations of native species, in which a range of rare and mostly functionally redundant plants proliferate after burning and prevent extensive invasion including a rapid conversion towards woodland. This research shows how biodiversity can be crucial for ecosystem stability despite appearing functionally insignificant beforehand, a relationship probably applicable to many ecosystems given the globally prevalent combination of intensive long-term land

Fungal-host diversity among mycoheterotrophic plants increases proportionally to their fungal-host overlap.

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Gomes, Sofia I F; Merckx, Vincent S F T; Saavedra, Serguei

2017-05-01

The vast majority of plants obtain an important proportion of vital resources from soil through mycorrhizal fungi. Generally, this happens in exchange of photosynthetically fixed carbon, but occasionally the interaction is mycoheterotrophic, and plants obtain carbon from mycorrhizal fungi. This process results in an antagonistic interaction between mycoheterotrophic plants and their fungal hosts. Importantly, the fungal-host diversity available for plants is restricted as mycoheterotrophic interactions often involve narrow lineages of fungal hosts. Unfortunately, little is known whether fungal-host diversity may be additionally modulated by plant-plant interactions through shared hosts. Yet, this may have important implications for plant competition and coexistence. Here, we use DNA sequencing data to investigate the interaction patterns between mycoheterotrophic plants and arbuscular mycorrhizal fungi. We find no phylogenetic signal on the number of fungal hosts nor on the fungal hosts shared among mycoheterotrophic plants. However, we observe a potential trend toward increased phylogenetic diversity of fungal hosts among mycoheterotrophic plants with increasing overlap in their fungal hosts. While these patterns remain for groups of plants regardless of location, we do find higher levels of overlap and diversity among plants from the same location. These findings suggest that species coexistence cannot be fully understood without attention to the two sides of ecological interactions.

Phylogeography, genetic diversity and demographic history of the ...

Indian Academy of Sciences (India)

Our data indicated that most of the Kurds mtDNA lineages belong to branches of the haplogroups with the Western Eurasian origin; with small fractions of the Eastern Eurasian and sub-Saharan African lineages. The low level of mtDNA diversity observed in the Havrami group presented a bias towards isolation or increased ...

Short communication: Conservation of Streptococcus uberis adhesion molecule and the sua gene in strains of Streptococcus uberis isolated from geographically diverse areas.

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Yuan, Ying; Dego, Oudessa Kerro; Chen, Xueyan; Abadin, Eurife; Chan, Shangfeng; Jory, Lauren; Kovacevic, Steven; Almeida, Raul A; Oliver, Stephen P

2014-12-01

The objective was to identify and sequence the sua gene (GenBank no. DQ232760; http://www.ncbi.nlm.nih.gov/genbank/) and detect Streptococcus uberis adhesion molecule (SUAM) expression by Western blot using serum from naturally S. uberis-infected cows in strains of S. uberis isolated in milk from cows with mastitis from geographically diverse areas of the world. All strains evaluated yielded a 4.4-kb sua-containing PCR fragment that was subsequently sequenced. Deduced SUAM AA sequences from those S. uberis strains evaluated shared >97% identity. The pepSUAM sequence located at the N terminus of SUAM was >99% identical among strains of S. uberis. Streptococcus uberis adhesion molecule expression was detected in all strains of S. uberis tested. These results suggest that sua is ubiquitous among strains of S. uberis isolated from diverse geographic locations and that SUAM is immunogenic. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Application of Pulsed Field Gel Electrophoresis for Study of Genetic Diversity in Mycobacterium tuberculosis Strains Isolated From Tuberculosis Patients.

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Khosravi, Azar Dokht; Vatani, Shideh; Feizabadi, Mohammad Mehdi; Abasi Montazeri, Effat; Jolodar, Abbas

2014-05-01

Mycobacterium tuberculosis genotyping can effectively improve tuberculosis (TB) control programs by controlling disease transmission. Pulsed field gel electrophoresis (PFGE) is a particularly powerful tool for determination of clonal identity of bacteria providing information for understanding and controlling the spread of disease. The aim of present study was to investigate the genetic diversity of M. tuberculosis strains in Khuzestan province by the PFGE technique. In total, 80 M. tuberculosis positive cultures were obtained from tuberculosis patients. PFGE was performed on 60 PCR-confirmed isolates by using DraI and XbaI restriction enzymes according to standard protocols. Plugs containing digested DNA were then loaded on agarose gels and run using contour-clamped homogenous electric fields. Fifty distinct DNA banding patterns were obtained by digestion of DNA with DraI and 38 DNA banding patterns by digestion with XbaI restriction enzymes. The patterns comprised of 17 different clusters in which cluster I was the major one, containing six strains. Three clusters contained three strains each and the 13 remaining clusters comprised of two strains each. Digestion with DraI yielded 15-20 DNA fragments with 50-485 kb size, while digestion by XbaI produced DNA fragments with a size smaller than 50-242 kb. Despite the ability of PFGE for study of genetic diversity of many mycobacterial species and it being considered as a robust and useful tool, in this study we only found a 15% epidemiological relationship amongst the isolates. Thus, for higher discrimination of genotypic clusters among M. tuberculosis clinical isolates, the application of more sophisticated complementary techniques is required.

Highways block gene flow and cause a rapid decline in genetic diversity of desert bighorn sheep

NARCIS (Netherlands)

Epps, CW; Palsboll, PJ; Wehausen, JD; Roderick, GK; Ramey, RR; McCullough, DR

2005-01-01

The rapid expansion of road networks has reduced connectivity among populations of flora and fauna. The resulting isolation is assumed to increase population extinction rates, in part because of the loss of genetic diversity. However, there are few cases where loss of genetic diversity has been

Enhanced interannual precipitation variability increases plant functional diversity that in turn ameliorates negative impact on productivity.

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Gherardi, Laureano A; Sala, Osvaldo E

2015-12-01

Although precipitation interannual variability is projected to increase due to climate change, effects of changes in precipitation variance have received considerable less attention than effects of changes in the mean state of climate. Interannual precipitation variability effects on functional diversity and its consequences for ecosystem functioning are assessed here using a 6-year rainfall manipulation experiment. Five precipitation treatments were switched annually resulting in increased levels of precipitation variability while maintaining average precipitation constant. Functional diversity showed a positive response to increased variability due to increased evenness. Dominant grasses decreased and rare plant functional types increased in abundance because grasses showed a hump-shaped response to precipitation with a maximum around modal precipitation, whereas rare species peaked at high precipitation values. Increased functional diversity ameliorated negative effects of precipitation variability on primary production. Rare species buffered the effect of precipitation variability on the variability in total productivity because their variance decreases with increasing precipitation variance. © 2015 John Wiley & Sons Ltd/CNRS.

Physiological and functional diversity of phenol degraders isolated from phenol-grown aerobic granules: Phenol degradation kinetics and trichloroethylene co-metabolic activities.

Science.gov (United States)

Zhang, Yi; Tay, Joo Hwa

2016-03-15

Aerobic granule is a novel form of microbial aggregate capable of degrading toxic and recalcitrant substances. Aerobic granules have been formed on phenol as the growth substrate, and used to co-metabolically degrade trichloroethylene (TCE), a synthetic solvent not supporting aerobic microbial growth. Granule formation process, rate limiting factors and the comprehensive toxic effects of phenol and TCE had been systematically studied. To further explore their potential at the level of microbial population and functions, phenol degraders were isolated and purified from mature granules in this study. Phenol and TCE degradation kinetics of 15 strains were determined, together with their TCE transformation capacities and other physiological characteristics. Isolation in the presence of phenol and TCE exerted stress on microbial populations, but the procedure was able to preserve their diversity. Wide variation was found with the isolates' kinetic behaviors, with the parameters often spanning 3 orders of magnitude. Haldane kinetics described phenol degradation well, and the isolates exhibited actual maximum phenol-dependent oxygen utilization rates of 9-449 mg DO g DW(-1) h(-1), in phenol concentration range of 4.8-406 mg L(-1). Both Michaelis-Menten and Haldane types were observed for TCE transformation, with the actual maximum rate of 1.04-21.1 mg TCE g DW(-1) h(-1) occurring between TCE concentrations of 0.42-4.90 mg L(-1). The TCE transformation capacities and growth yields on phenol ranged from 20-115 mg TCE g DW(-1) and 0.46-1.22 g DW g phenol(-1), respectively, resulting in TCE transformation yields of 10-70 mg TCE g phenol(-1). Contact angles of the isolates were between 34° and 82°, suggesting both hydrophobic and hydrophilic cell surface. The diversity in the isolates is a great advantage, as it enables granules to be versatile and adaptive under different operational conditions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Increased spontaneous MEG signal diversity for psychoactive doses of ketamine, LSD and psilocybin

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Schartner, Michael M.; Carhart-Harris, Robin L.; Barrett, Adam B.; Seth, Anil K.; Muthukumaraswamy, Suresh D.

2017-04-01

What is the level of consciousness of the psychedelic state? Empirically, measures of neural signal diversity such as entropy and Lempel-Ziv (LZ) complexity score higher for wakeful rest than for states with lower conscious level like propofol-induced anesthesia. Here we compute these measures for spontaneous magnetoencephalographic (MEG) signals from humans during altered states of consciousness induced by three psychedelic substances: psilocybin, ketamine and LSD. For all three, we find reliably higher spontaneous signal diversity, even when controlling for spectral changes. This increase is most pronounced for the single-channel LZ complexity measure, and hence for temporal, as opposed to spatial, signal diversity. We also uncover selective correlations between changes in signal diversity and phenomenological reports of the intensity of psychedelic experience. This is the first time that these measures have been applied to the psychedelic state and, crucially, that they have yielded values exceeding those of normal waking consciousness. These findings suggest that the sustained occurrence of psychedelic phenomenology constitutes an elevated level of consciousness - as measured by neural signal diversity.

Genetic and phenotypic diversity of naturally isolated wild strains of Aspergillus niger with hyper glucose oxidase production

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MAHMOUD EL-HARIRI

2015-12-01

Full Text Available Glucose oxidase (GOx is the basic stone for many of biological industry worldwide. The improvement of GOx production basically depends on selection of hyper producer strain of Aspergillus niger. Selective isolation and screening for natural hyper producer strains of A. niger and sequence analysis of the GOD gene, which is responsible for production of the enzyme, are very effective approaches to investigate the naturally modified strains of A. niger with hyper productive capacity of GOx enzyme. The aims of the current study were selective isolation of naturally hyper GOx producing strains of A. niger and evaluation of their GOx activities under optimized parameters in the laboratory. Five wild Egyptian isolates of A. niger were screened for GOx and catalase activity using two types of modified basal liquid media. The GOx activity was evaluated by high throughout liquid phase system. The isolates showed a variable activity for GOx production ranged from 0 to 28.7 U.ml-1. One isolate coded Strain 7 was negative GOx producer on Vogel's broth medium in comparison to other isolates, while its GOx activity on Cazpek Dox was considered as positive (7.28 U.ml-1. It was concluded that GOx production is affected by three controllable factors – the basal media components, time of incubation, and the strain with its adaption to the media components‎. Also, the catalase activity was tested and it was produced with a different degree of variability, which may be reflected on GOx stability. GOD genes of these wild variant of A. niger were cloned and sequenced to determine intraspecies diversity of GOD between the wild variants. The comparison of isolated wild variants to other reference hyper GOx producer strains of A. niger was performed to determine if the GOD sequence analysis of these strains can be distinguished based on their GOx activity. This is the first report for isolation and detection of naturally A. niger hyper GOx-producer strains with

Genetic Diversity of Plasmodium falciparum Field Isolates in Central Sudan Inferred by PCR Genotyping of Merozoite Surface Protein 1 and 2.

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Hamid, Muzamil M Abdel; Mohammed, Sara B; El Hassan, Ibrahim M

2013-02-01

Characterization of Plasmodium falciparum diversity is commonly achieved by amplification of the polymorphic regions of the merozoite surface proteins 1 (MSP1) and 2 (MSP2) genes. The present study aimed to determine the allelic variants distribution of MSP1 and MSP2 and multiplicity of infection in P. falciparum field isolates from Kosti, central Sudan, an area characterized by seasonal malaria transmission. Total 121 samples (N = 121) were collected during a cross-sectional survey between March and April 2003. DNA was extracted and MSP1 and MSP2 polymorphic loci were genotyped. The total number of alleles identified in MSP1 block 2 was 11, while 16 alleles were observed in MSP2 block 3. In MSP1, RO33 was found to be the predominant allelic type, carried alone or in combination with MAD20 and K1 types, whereas FC27 family was the most prevalent in MSP2. Sixty two percent of isolates had multiple genotypes and the overall mean multiplicity of infection was 1.93 (CI 95% 1.66-2.20). Age correlated with parasite density (P = 0.017). In addition, a positive correlation was observed between parasite densities and the number of alleles (P = 0.022). Genetic diversity in P. falciparum field isolates in central Sudan was high and consisted of multiple clones.

Dramatic increases of soil microbial functional gene diversity at the treeline ecotone of Changbai Mountain

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Congcong Shen

2016-07-01

Full Text Available The elevational and latitudinal diversity patterns of microbial taxa have attracted great attention in the past decade. Recently, the distribution of functional attributes has been in the spotlight. Here, we report a study profiling soil microbial communities along an elevation gradient (500 to 2200 m on Changbai Mountain. Using a comprehensive functional gene microarray (GeoChip 5.0, we found that microbial functional gene richness exhibited a dramatic increase at the treeline ecotone, but the bacterial taxonomic and phylogenetic diversity based on 16S rRNA gene sequencing did not exhibit such a similar trend. However, the β-diversity (compositional dissimilarity among sites for both bacterial taxa and functional genes was similar, showing significant elevational distance-decay patterns which presented increased dissimilarity with elevation. The bacterial taxonomic diversity/structure was strongly influenced by soil pH, while the functional gene diversity/structure was significantly correlated with soil dissolved organic carbon (DOC. This finding highlights that soil DOC may be a good predictor in determining the elevational distribution of microbial functional genes. The finding of significant shifts in functional gene diversity at the treeline ecotone could also provide valuable information for predicting the responses of microbial functions to climate change.

Combining phylogenetic and demographic inferences to assess the origin of the genetic diversity in an isolated wolf population.

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Luca Montana

Full Text Available The survival of isolated small populations is threatened by both demographic and genetic factors. Large carnivores declined for centuries in most of Europe due to habitat changes, overhunting of their natural prey and direct persecution. However, the current rewilding trends are driving many carnivore populations to expand again, possibly reverting the erosion of their genetic diversity. In this study we reassessed the extent and origin of the genetic variation of the Italian wolf population, which is expanding after centuries of decline and isolation. We genotyped wolves from Italy and other nine populations at four mtDNA regions (control-region, ATP6, COIII and ND4 and 39 autosomal microsatellites. Results of phylogenetic analyses and assignment procedures confirmed in the Italian wolves a second private mtDNA haplotype, which belongs to a haplogroup distributed mostly in southern Europe. Coalescent analyses showed that the unique mtDNA haplotypes in the Italian wolves likely originated during the late Pleistocene. ABC simulations concordantly showed that the extant wolf populations in Italy and in south-western Europe started to be isolated and declined right after the last glacial maximum. Thus, the standing genetic variation in the Italian wolves principally results from the historical isolation south of the Alps.

Limited genetic diversity among Sarcocystis neurona strains infecting southern sea otters precludes distinction between marine and terrestrial isolates.

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Wendte, J M; Miller, M A; Nandra, A K; Peat, S M; Crosbie, P R; Conrad, P A; Grigg, M E

2010-04-19

Sarcocystis neurona is an apicomplexan parasite identified as a cause of fatal neurological disease in the threatened southern sea otter (Enhydra lutris nereis). In an effort to characterize virulent S. neurona strains circulating in the marine ecosystem, this study developed a range of markers relevant for molecular genotyping. Highly conserved sequences within the 18S ribosomal gene array, the plastid-encoded RNA polymerase (RPOb) and the cytochrome c oxidase subunit 1 mitochondrial gene (CO1) were assessed for their ability to distinguish isolates at the genus and species level. For within-species comparisons, five surface antigens (SnSAG1-SnSAG5) and one high resolution microsatellite marker (Sn9) were developed as genotyping markers to evaluate intra-strain diversity. Molecular analysis at multiple loci revealed insufficient genetic diversity to distinguish terrestrial isolates from strains infecting marine mammals. Furthermore, SnSAG specific primers applied against DNA from the closely related species, Sarcocystis falcatula, lead to the discovery of highly similar orthologs to SnSAG2, 3, and 4, calling into question the specificity of diagnostic tests based on these antigens. The results of this study suggest a population genetic structure for S. neurona similar to that reported for the related parasite, Toxoplasma gondii, dominated by a limited number of successful genotypes. Published by Elsevier B.V.

Antimicrobial Resistance and Genotypic Diversity of Campylobacter Isolated from Pig, Dairy and Beef Cattle in Tanzania

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Isaac eKashoma

2015-11-01

Full Text Available Foodborne Campylobacter infections pose a serious threat to public health worldwide. However, the occurrence and characteristics of Campylobacter in food animals and products remain largely unknown in Tanzania. The objective of this study was to determine the prevalence, antibiotic resistance, and genetic profiles (sequence types, STs of Campylobacter isolated from feces of pigs and dairy and beef cattle in Tanzania. Overall, 259 (~ 30% of 864 samples were positive for Campylobacter spp, which were detected in 32.5%, 35.4%, and 19.6% of the pig, dairy, and beef cattle samples, respectively. Multiplex PCR analysis identified 64.5% and 29.3% of the Campylobacter isolates as C. coli and C. jejuni, respectively. The majority (91.9% of the isolates from pig samples were identified as C. coli, while C. jejuni accounted for 65.5% of the isolates from cattle. Antimicrobial susceptibility testing using the disk diffusion assay and the broth microdilution method revealed resistance to: ampicillin (70% and 76%, gentamicin (1.8% and 12.6%, respectively, streptomycin (65.8% and 74.8%, erythromycin (41.4% and 48.7%, tetracycline (18.9% and 23.4%, and ciprofloxacin (14.4% and 7.2%. Resistance to nalidixic acid (39.6%, azithromycin (13.5%, and chloramphenicol (4.5% was determined using the disk diffusion assay only, while resistance to tylosin (38.7% was quantified using the broth microdilution method. Multilocus sequence typing of 111 Campylobacter isolates resulted in the identification of 48 STs (26 C. jejuni and 22 C. coli of which 7 were novel (6 C. jejuni and 1 C. coli. Taken together, this study revealed the high prevalence, genetic diversity and antimicrobial resistance of Campylobacter in important food animals in Tanzania, which highlights the urgent need for the surveillance and control of Campylobacter in this country.

Genetic diversity and antimicrobial resistance of Yersinia enterocolitica isolated from pigs and humans in Lithuania.

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Novoslavskij, Aleksandr; Kudirkienė, Eglė; Marcinkutė, Audronė; Bajoriūnienė, Almina; Korkeala, Hannu; Malakauskas, Mindaugas

2013-06-01

Yersiniosis is one of the three leading foodborne zoonoses in Lithuania, and the incidence of 12.86 per 100,000 population was the highest among EU member states in 2010. Contaminated pig carcasses and subsequently undercooked pig meat are considered to be the primary transmission vehicle of enteropathogenic Y. enterocolitica to consumers. With the aim of evaluating pigs as a possible source of human yersiniosis in Lithuania, this study investigated the genetic diversity of Y. enterocolitica isolated from pigs and human cases of yersiniosis. In addition, the antimicrobial resistance of selected isolates from both sources was compared. In total, 83 Y. enterocolitica strains were characterised using pulsed field gel electrophoresis. Overall, 68% of Y. enterocolitica 4/O:3 pulsotypes found in human clinical samples were identical to 81% of pulsotypes found in the pig production chain. Yersinia enterocolitica pulsotype II was confirmed as the dominant pulsotype in the pig production chain and was identical to nine of 19 Y. enterocolitica strains found in humans. All tested Y. enterocolitica 4/O:3 strains were resistant to ampicillin and erythromycin and sensitive to ciprofloxacin. Of the strains studied, 5% were resistant to tetracycline and streptomycin. This study showed that pigs may be the main source of human yersiniosis in Lithuania. In addition, Y. enterocolitica 4/O:3 strains isolated from the pig production chain and from yersiniosis patients shared similar resistance to different antimicrobials. © 2012 Society of Chemical Industry.

Prevalence, Virulence Genes, Antimicrobial Susceptibility, and Genetic Diversity of Bacillus cereus Isolated From Pasteurized Milk in China

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Tiantian Gao

2018-03-01

Full Text Available Bacillus cereus is a common and important food-borne pathogen that can be found in various food products. Due to low-temperature sterilization for a short period of time, pasteurization is not sufficient for complete elimination of B. cereus in milk, thereby cause severe economic loss and food safety problems. It is therefore of paramount importance to perform risk assessment of B. cereus in pasteurized milk. In this study, we isolated B. cereus from pasteurized milk samples in different regions of China, and evaluated the contamination situation, existence of virulence genes, antibiotic resistance profile and genetic polymorphism of B. cereus isolates. Intriguingly, 70 samples (27% were found to be contaminated by B. cereus and the average contamination level was 111 MPN/g. The distribution of virulence genes was assessed toward 10 enterotoxigenic genes (hblA, hblC, hblD, nheA, nheB, nheC, cytK, entFM, bceT, and hlyII and one emetic gene (cesB. Forty five percent strains harbored enterotoxigenic genes hblACD and 93% isolates contained nheABC gene cluster. The positive rate of cytK, entFM, bceT, hlyII, and cesB genes were 73, 96, 75, 54, and 5%, respectively. Antibiotic susceptibility assessment showed that most of the isolates were resistant to β-lactam antibiotics and rifampicin, but susceptible to other antibiotics such as ciprofloxacin, gentamicin and chloramphenicol. Total multidrug-resistant population was about 34%. In addition, B. cereus isolates in pasteurized milk showed a high genetic diversity. In conclusion, our findings provide the first reference on the prevalence, contamination level and characteristics of B. cereus isolated from pasteurized milk in China, suggesting a potential high risk of B. cereus to public health and dairy industry.

MULTILOCUS SEQUENCE TYPING OF BRUCELLA ISOLATES FROM THAILAND.

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Chawjiraphan, Wireeya; Sonthayanon, Piengchan; Chanket, Phanita; Benjathummarak, Surachet; Kerdsin, Anusak; Kalambhaheti, Thareerat

2016-11-01

Although brucellosis outbreaks in Thailand are rare, they cause abortions and infertility in animals, resulting in significant economic loss. Because Brucella spp display > 90% DNA homology, multilocus sequence typing (MLST) was employed to categorize local Brucella isolates into sequence types (STs) and to determine their genetic relatedness. Brucella samples were isolated from vaginal secretion of cows and goats, and from blood cultures of infected individuals. Brucella species were determined by multiplex PCR of eight loci, in addition to MLST based on partial DNA sequences of nine house-keeping genes. MLST analysis of 36 isolates revealed 78 distinct novel allele types and 34 novel STs, while two isolates possessed the known ST8. Sequence alignments identified polymorphic sites in each allele, ranging from 2-6%, while overall genetic diversity was 3.6%. MLST analysis of the 36 Brucella isolates classified them into three species, namely, B. melitensis, B. abortus and B. suis, in agreement with multiplex PCR results. Genetic relatedness among ST members of B. melitensis and B. abortus determined by eBURST program revealed ST2 as founder of B. abortus isolates and ST8 the founder of B. melitensis isolates. ST 36, 41 and 50 of Thai Brucella isolates were identified as single locus variants of clonal cluster (CC) 8, while the majority of STs were diverse. The genetic diversity and relatedness identified using MLST revealed hitherto unexpected diversity among Thai Brucella isolates. Genetic classification of isolates could reveal the route of brucellosis transmission among humans and farm animals and also reveal their relationship with other isolates in the region and other parts of the world.

Impacts of varying light regimes on phycobiliproteins of Nostoc sp. HKAR-2 and Nostoc sp. HKAR-11 isolated from diverse habitats.

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Kannaujiya, Vinod K; Sinha, Rajeshwar P

2015-11-01

The adaptability of cyanobacteria in diverse habitats is an important factor to withstand harsh conditions. In the present investigation, the impacts of photosynthetically active radiation (PAR; 400-700 nm), ultraviolet-B (UV-B; 280-315 nm), and PAR + UV-B radiations on two cyanobacteria viz., Nostoc sp. HKAR-2 and Nostoc sp. HKAR-11 inhabiting diverse habitats such as hot springs and rice fields, respectively, were studied. Cell viability was about 14 % in Nostoc sp. HKAR-2 and Nostoc sp. HKAR-11 after 48 h of UV-B exposure. PAR had negligible negative impact on the survival of both cyanobacteria. The continuous exposure of UV-B and PAR + UV-B showed rapid uncoupling, bleaching, fragmentation, and degradation in both phycocyanin (C-PC) and phycoerythrin (C-PE) subunits of phycobiliproteins (PBPs). Remarkable bleaching effect of C-PE and C-PC was not only observed with UV-B or PAR + UV-B radiation, but longer period (24-48 h) of exposure with PAR alone also showed noticeable negative impact. The C-PE and C-PC subunits of the rice field isolate Nostoc sp. HKAR-11 were severely damaged in comparison to the hot spring isolate Nostoc sp. HKAR-2 with rapid wavelength shifting toward shorter wavelengths denoting the bleaching of both the accessory light harvesting pigments. The results indicate that PBPs of the hot spring isolate Nostoc sp. HKAR-2 were more stable under various light regimes in comparison to the rice field isolate Nostoc sp. HKAR-11 that could serve as a good source of valuable pigments to be used in various biomedical and biotechnological applications.

Rethinking the Structure of Student Recruitment and Efforts to Increase Racial and Ethnic Diversity in Doctoral Education

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Kimberly A. Griffin

2015-07-01

Full Text Available While researchers, institutional leaders, and policymakers have made significant progress towards increasing undergraduate student diversity in the United States, diversity in graduate education has been less often studied and a more challenging goal on which to make progress. This qualitative study explores the roles and work of graduate diversity officers (GDOs in student recruitment activities with a focus on how race and issues of diversity manifest and influence this process. Interviews with fourteen GDOs at 11 different research universities in the United States highlight the phases in the graduate recruitment process, the manner in which diversity is considered at each stage, and GDOs’ perceptions of their ability to shape this process. Findings suggest that GDOs are important institutional agents in diversification efforts; however, faculty engagement and broad institutional commitment are required to increase diversity in graduate education due to GDOs’ often limited involvement in the admissions stage of the recruitment process, where race becomes the most salient in decision making.

Genotypic and phenotypic diversity of Ralstonia pickettii and Ralstonia insidiosa isolates from clinical and environmental sources including High-purity Water.

LENUS (Irish Health Repository)

Ryan, Michael P

2011-08-30

Abstract Background Ralstonia pickettii is a nosocomial infectious agent and a significant industrial contaminant. It has been found in many different environments including clinical situations, soil and industrial High Purity Water. This study compares the phenotypic and genotypic diversity of a selection of strains of Ralstonia collected from a variety of sources. Results Ralstonia isolates (fifty-nine) from clinical, industrial and environmental origins were compared genotypically using i) Species-specific-PCR, ii) PCR and sequencing of the 16S-23S rRNA Interspatial region (ISR) iii) the fliC gene genes, iv) RAPD and BOX-PCR and v) phenotypically using biochemical testing. The species specific-PCR identified fifteen out of fifty-nine designated R. pickettii isolates as actually being the closely related species R. insidiosa. PCR-ribotyping of the 16S-23S rRNA ISR indicated few major differences between the isolates. Analysis of all isolates demonstrated different banding patterns for both the RAPD and BOX primers however these were found not to vary significantly. Conclusions R. pickettii species isolated from wide geographic and environmental sources appear to be reasonably homogenous based on genotypic and phenotypic characteristics. R. insidiosa can at present only be distinguished from R. pickettii using species specific PCR. R. pickettii and R. insidiosa isolates do not differ significantly phenotypically or genotypically based on environmental or geographical origin.

Prevalence and Genetic Diversity of Enterococcus faecalis Isolates from Mineral Water and Spring Water in China

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Lei Wei

2017-06-01

Full Text Available Enterococcus faecalis is an important opportunistic pathogen which is frequently detected in mineral water and spring water for human consumption and causes human urinary tract infections, endocarditis and neonatal sepsis. The aim of this study was to determine the prevalence, virulence genes, antimicrobial resistance and genetic diversity of E. faecalis from mineral water and spring water in China. Of 314 water samples collected from January 2013 to January 2014, 48 samples (15.3% were contaminated E. faecalis. The highest contamination rate occurred in activated carbon filtered water of spring water (34.5%, followed by source water of spring water (32.3% and source water of mineral water (6.4%. The virulence gene test of 58 E. faecalis isolates showed that the detection rates of asa1, ace, cylA, gelE and hyl were 79.3, 39.7, 0, 100, 0%, respectively. All 58 E. faecalis isolates were not resistant to 12 kinds of antibiotics (penicillin, ampicillin, linezolid, quinupristin/dalfopristin, vancomycin, gentamicin, streptomycin, ciprofloxacin, levofloxacin, norfloxacin, nitrofurantoin, and tetracycline. Enterobacterial repetitive intergenic consensus-PCR classified 58 isolates and three reference strains into nine clusters with a similarity of 75%. This study is the first to investigate the prevalence of E. faecalis in mineral water and spring water in China. The results of this study suggested that spring water could be potential vehicles for transmission of E. faecalis.

Diversity of Staphylococcus aureus Isolates in European Wildlife

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Monecke, Stefan; Gavier-Widén, Dolores; Hotzel, Helmut; Peters, Martin; Guenther, Sebastian; Lazaris, Alexandros; Loncaric, Igor; Müller, Elke; Reissig, Annett; Ruppelt-Lorz, Antje; Shore, Anna C.; Walter, Birgit; Coleman, David C.; Ehricht, Ralf

2016-01-01

Staphylococcus aureus is a well-known colonizer and cause of infection among animals and it has been described from numerous domestic and wild animal species. The aim of the present study was to investigate the molecular epidemiology of S. aureus in a convenience sample of European wildlife and to review what previously has been observed in the subject field. 124 S. aureus isolates were collected from wildlife in Germany, Austria and Sweden; they were characterized by DNA microarray hybridization and, for isolates with novel hybridization patterns, by multilocus sequence typing (MLST). The isolates were assigned to 29 clonal complexes and singleton sequence types (CC1, CC5, CC6, CC7, CC8, CC9, CC12, CC15, CC22, CC25, CC30, CC49, CC59, CC88, CC97, CC130, CC133, CC398, ST425, CC599, CC692, CC707, ST890, CC1956, ST2425, CC2671, ST2691, CC2767 and ST2963), some of which (ST2425, ST2691, ST2963) were not described previously. Resistance rates in wildlife strains were rather low and mecA-MRSA isolates were rare (n = 6). mecC-MRSA (n = 8) were identified from a fox, a fallow deer, hares and hedgehogs. The common cattle-associated lineages CC479 and CC705 were not detected in wildlife in the present study while, in contrast, a third common cattle lineage, CC97, was found to be common among cervids. No Staphylococcus argenteus or Staphylococcus schweitzeri-like isolates were found. Systematic studies are required to monitor the possible transmission of human- and livestock-associated S. aureus/MRSA to wildlife and vice versa as well as the possible transmission, by unprotected contact to animals. The prevalence of S. aureus/MRSA in wildlife as well as its population structures in different wildlife host species warrants further investigation. PMID:27992523

Abundance, genetic diversity and sensitivity to demethylation inhibitor fungicides of Aspergillus fumigatus isolates from organic substrates with special emphasis on compost.

Science.gov (United States)

Santoro, Karin; Matić, Slavica; Gisi, Ulrich; Spadaro, Davide; Pugliese, Massimo; Gullino, Maria L

2017-12-01

Aspergillus fumigatus is a widespread fungus that colonizes dead organic substrates but it can also cause fatal human diseases. Aspergilloses are treated with demethylation inhibitor (DMI) fungicides; however, resistant isolates appeared recently in the medical and also environmental area. The present study aims at molecular characterizing and quantifying A. fumigatus in major environmental habitats and determining its sensitivity to medical and agricultural DMI fungicides. A. fumigatus was isolated only rarely from soil and meadow/forest organic matter but high concentrations (10 3 to 10 7  cfu/g) were detected in substrates subjected to elevated temperatures, such as compost and silage. High genetic diversity of A. fumigatus from compost was found based on SSR markers, distinguishing among fungal isolates even when coming from the same substrate sample, while subclustering was observed based on mutations in cyp51A gene. Several cyp51A amino acid substitutions were found in 15 isolates, although all isolates were fully sensitive to the tested DMI fungicides, with exception of one isolate in combination with one fungicide. This study suggests that the tested A. fumigatus isolates collected in Italy, Spain and Hungary from the fungus' major living habitats (compost) and commercial growing substrates are not potential carriers for DMI resistance in the environment. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Rapid growth and genetic diversity retention in an isolated reintroduced black bear population in the central appalachians

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Murphy, Sean M.; Cox, John J.; Clark, Joseph D.; Augustine, Benjamin J.; Hast, John T.; Gibbs, Dan; Strunk, Michael; Dobey, Steven

2015-01-01

Animal reintroductions are important tools of wildlife management to restore species to their historical range, and they can also create unique opportunities to study population dynamics and genetics from founder events. We used non-invasive hair sampling in a systematic, closed-population capture-mark-recapture (CMR) study design at the Big South Fork (BSF) area in Kentucky during 2010 and Tennessee during 2012 to estimate the demographic and genetic characteristics of the black bear (Ursus americanus) population that resulted from a reintroduced founding population of 18 bears in 1998. We estimated 38 (95% CI: 31–66) and 190 (95% CI: 170–219) bears on the Kentucky and Tennessee study areas, respectively. Based on the Tennessee abundance estimate alone, the mean annual growth rate was 18.3% (95% CI: 17.4–19.5%) from 1998 to 2012. We also compared the genetic characteristics of bears sampled during 2010–2012 to bears in the population during 2000–2002, 2–4 years following reintroduction, and to the source population. We found that the level of genetic diversity since reintroduction as indicated by expected heterozygosity (HE) remained relatively constant (HE(source, 2004) = 0.763, HE(BSF, 2000–2002) = 0.729, HE(BSF, 2010–2012) = 0.712) and the effective number of breeders (NB) remained low but had increased since reintroduction in the absence of sufficient immigration (NB(BSF, 2000–2002) = 12, NB(BSF, 2010–2012)  = 35). This bear population appears to be genetically isolated, but contrary to our expectations, we did not find evidence of genetic diversity loss or other deleterious genetic effects typically observed from small founder groups. We attribute that to high initial genetic diversity in the founder group combined with overlapping generations and rapid population growth. Although the population remains relatively small, the reintroduction using a small founder group appears to be demographically and genetically

Genetic diversity of clinical and environmental isolates of Vibrio cholerae determined by amplified fragment length polymorphism fingerprinting.

Science.gov (United States)

Jiang, S C; Matte, M; Matte, G; Huq, A; Colwell, R R

2000-01-01

Vibrio cholerae, the causative agent of major epidemics of diarrheal disease in Bangladesh, South America, Southeastern Asia, and Africa, was isolated from clinical samples and from aquatic environments during and between epidemics over the past 20 years. To determine the evolutionary relationships and molecular diversity of these strains, in order to understand sources, origin, and epidemiology, a novel DNA fingerprinting technique, amplified fragment length polymorphism (AFLP), was employed. Two sets of restriction enzyme-primer combinations were tested for fingerprinting of V. cholerae serogroup O1, O139, and non-O1, O139 isolates. Amplification of HindIII- and TaqI-digested genomic DNA produced 30 to 50 bands for each strain. However, this combination, although capable of separating environmental isolates of O1 and non-O1 strains, was unable to distinguish between O1 and O139 clinical strains. This result confirmed that clinical O1 and O139 strains are genetically closely related. On the other hand, AFLP analyses of restriction enzyme ApaI- and TaqI-digested genomic DNA yielded 20 to 30 bands for each strain, but were able to separate O1 from O139 strains. Of the 74 strains examined with the latter combination, 26 serogroup O1 strains showed identical banding patterns and were represented by the O1 El Tor strain of the seventh pandemic. A second group, represented by O139 Bengal, included 12 strains of O139 clinical isolates, with 7 from Thailand, 3 from Bangladesh, and 2 from India. Interestingly, an O1 clinical isolate from Africa also grouped with the O139 clinical isolates. Eight clinical O1 isolates from Mexico grouped separately from the O1 El Tor of the seventh pandemic, suggesting an independent origin of these isolates. Identical fingerprints were observed between an O1 environmental isolate from a river in Chile and an O1 clinical strain from Kenya, both isolated more than 10 years apart. Both strains were distinct from the O1 seventh pandemic strain

Ibrutinib Therapy Increases T Cell Repertoire Diversity in Patients with Chronic Lymphocytic Leukemia.

Science.gov (United States)

Yin, Qingsong; Sivina, Mariela; Robins, Harlan; Yusko, Erik; Vignali, Marissa; O'Brien, Susan; Keating, Michael J; Ferrajoli, Alessandra; Estrov, Zeev; Jain, Nitin; Wierda, William G; Burger, Jan A

2017-02-15

The Bruton's tyrosine kinase inhibitor ibrutinib is a highly effective, new targeted therapy for chronic lymphocytic leukemia (CLL) that thwarts leukemia cell survival, growth, and tissue homing. The effects of ibrutinib treatment on the T cell compartment, which is clonally expanded and thought to support the growth of malignant B cells in CLL, are not fully characterized. Using next-generation sequencing technology, we characterized the diversity of TCRβ-chains in peripheral blood T cells from 15 CLL patients before and after 1 y of ibrutinib therapy. We noted elevated CD4 + and CD8 + T cell numbers and a restricted TCRβ repertoire in all pretreatment samples. After 1 y of ibrutinib therapy, elevated peripheral blood T cell numbers and T cell-related cytokine levels had normalized, and T cell repertoire diversity increased significantly. Dominant TCRβ clones in pretreatment samples declined or became undetectable, and the number of productive unique clones increased significantly during ibrutinib therapy, with the emergence of large numbers of low-frequency TCRβ clones. Importantly, broader TCR repertoire diversity was associated with clinical efficacy and lower rates of infections during ibrutinib therapy. These data demonstrate that ibrutinib therapy increases diversification of the T cell compartment in CLL patients, which contributes to cellular immune reconstitution. Copyright © 2017 by The American Association of Immunologists, Inc.

Commentary: Diversity 3.0: a necessary systems upgrade.

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Nivet, Marc A

2011-12-01

This is a defining moment for health and health care in the United States, and medical schools and teaching hospitals have a critical role to play. The combined forces of health care reform, demographic shifts, continued economic woes, and the projected worsening of physician shortages portend major challenges for the health care enterprise in the near future. In this commentary, the author employs a diversity framework implemented by IBM and argues that this framework should be adapted to an academic medicine setting to meet the challenges to the health care enterprise. Using IBM's diversity framework, the author explores three distinct phases in the evolution of diversity thinking within the academic medicine community. The first phase included isolated efforts aimed at removing social and legal barriers to access and equality, with institutional excellence and diversity as competing ends. The second phase kept diversity on the periphery but raised awareness about how increasing diversity benefits everyone, allowing excellence and diversity to exist as parallel ends. In the third phase, which is emerging today and reflects a growing understanding of diversity's broader relevance to institutions and systems, diversity and inclusion are integrated into the core workings of the institution and framed as integral for achieving excellence. The Association of American Medical Colleges, a leading voice and advocate for increased student and faculty diversity, is set to play a more active role in building the capacity of the nation's medical schools and teaching hospitals to move diversity from a periphery to a core strategy.

Increased cefepime MIC for enterobacteriacae clinical isolates.

Science.gov (United States)

Najafi, Narges; Alikhani, Ahmad; Babamahmoudi, Farhang; Davoudi, Alireza; Ghasemiyan, Roya; Aliyan, Shahriar; Shoujaiifar, Arman

2013-01-01

Background : Cefepime was used as empirical treatment in ventilator-associated pneumonia (VAP) induced by gram-negative and gram-positive bacteria. This study aimed to determine the antimicrobial susceptibility pattern of cefepime against microorganism causing VAP in Mazandaran, North of Iran. This study was performed on VAP patients diagnosed with clinical pulmonary infection score (CPIS) scores in ICU of two hospitals. For each patient suspected of having VAP, quantitative culture of endotracheal aspiration (QEA) was performed and MIC was determined by micro dilution test. Data were collected and analyzed. Thirty- five cases of enterobacteriaceae were isolated orderly including E coli 13, P. aeruginosa 11, Enterobacter 7 and K. pneumonia 4 cases. All the isolated E. coli, Enterobacter and Klebsiella, 54.5% of P. aeruginosa isolated were fully resistant to cefepime. The results of this study show that cefepime is not a reasonable choice for empirical treatment of nosocomial pneumonia and VAP.

Diversity of halophilic archaea from six hypersaline environments in Turkey.

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Ozcan, Birgul; Ozcengiz, Gulay; Coleri, Arzu; Cokmus, Cumhur

2007-06-01

The diversity of archaeal strains from six hypersaline environments in Turkey was analyzed by comparing their phenotypic characteristics and 16S rDNA sequences. Thirty-three isolates were characterized in terms of their phenotypic properties including morphological and biochemical characteristics, susceptibility to different antibiotics, and total lipid and plasmid contents, and finally compared by 16S rDNA gene sequences. The results showed that all isolates belong to the family Halobacteriaceae. Phylogenetic analyses using approximately 1,388 bp comparisions of 16S rDNA sequences demonstrated that all isolates clustered closely to species belonging to 9 genera, namely Halorubrum (8 isolates), Natrinema (5 isolates), Haloarcula (4 isolates), Natronococcus (4 isolates), Natrialba (4 isolates), Haloferax (3 isolates), Haloterrigena (3 isolates), Halalkalicoccus (1 isolate), and Halomicrobium (1 isolate). The results revealed a high diversity among the isolated halophilic strains and indicated that some of these strains constitute new taxa of extremely halophilic archaea.

Bovine viral diarrhea virus (BVDV) genetic diversity in Spain: A review

International Nuclear Information System (INIS)

Diéguez, F.J.; Cerviño, M.; Yus, E.

2017-01-01

Bovine viral diarrhea virus (BVDV), a member of the genus Pestivirus of the family Flaviviridae, causes significant losses in cattle farming worldwide because of reduced milk production, increased mortality of young animals and reproductive, respiratory and intestinal problems. The virus is characterized by an important genetic, and consequently antigenic and pathogenic diversity. Knowing the variability of viral strains present in a population provides valuable information, particularly relevant for control programs development, vaccination recommendations and even identification of likely infection sources. Such information is therefore important at both local and regional levels. This review focuses on the genetic diversity of BVDV isolates infecting cattle in Spain over the last years. According to the published data, the most prevalent BVDV group in Spain was 1b, and to a lesser extent 1d, 1e and 1f. Besides, BVDV-2 has also been found in Spain with several ratified isolates. The studies carried out in Spain also showed increased genetic heterogeneity of BVDV strains, possibly due to a more intensive use of analytical tools available, presenting studies with increasingly greater sample sizes.

Bovine viral diarrhea virus (BVDV) genetic diversity in Spain: A review

Energy Technology Data Exchange (ETDEWEB)

Diéguez, F.J.; Cerviño, M.; Yus, E.

2017-07-01

Bovine viral diarrhea virus (BVDV), a member of the genus Pestivirus of the family Flaviviridae, causes significant losses in cattle farming worldwide because of reduced milk production, increased mortality of young animals and reproductive, respiratory and intestinal problems. The virus is characterized by an important genetic, and consequently antigenic and pathogenic diversity. Knowing the variability of viral strains present in a population provides valuable information, particularly relevant for control programs development, vaccination recommendations and even identification of likely infection sources. Such information is therefore important at both local and regional levels. This review focuses on the genetic diversity of BVDV isolates infecting cattle in Spain over the last years. According to the published data, the most prevalent BVDV group in Spain was 1b, and to a lesser extent 1d, 1e and 1f. Besides, BVDV-2 has also been found in Spain with several ratified isolates. The studies carried out in Spain also showed increased genetic heterogeneity of BVDV strains, possibly due to a more intensive use of analytical tools available, presenting studies with increasingly greater sample sizes.

Population structure and diversity of citrus tristeza virus (CTV) isolates in Hunan province, China.

Science.gov (United States)

Xiao, Cui; Yao, Run-Xian; Li, Fang; Dai, Su-Ming; Licciardello, Grazia; Catara, Antonino; Gentile, Alessandra; Deng, Zi-Niu

2017-02-01

Stem-pitting (SP) is the main type of citrus tristeza virus (CTV) that causes severe damage to citrus trees, especially those of sweet orange, in Hunan province, China. Understanding the local CTV population structure should provide clues for effective mild strain cross-protection (MSCP) of the SP strain of CTV. In this study, markers for the p23 gene, multiple molecular markers (MMMs), and sequence analysis of the three silencing suppressor genes (p20, p23 and p25) were employed to analyze the genetic diversity and genotype composition of the CTV population based on 51 CTV-positive samples collected from 14 citrus orchards scattered around six major citrus-growing areas of Hunan. The results indicated that the CTV population structure was extremely complex and that infection was highly mixed. In total, p23 gene markers resulted in six profiles, and MMMs demonstrated 25 profiles. The severe VT and T3 types appeared to be predominantly associated with SP, while the mild T30 and RB types were related to asymptomatic samples. Based on phylogenetic analysis of the amino acid sequences of p20, p23 and p25, 19 representative CTV samples were classified into seven recently established CTV groups and a potentially novel one. A high level of genetic diversity, as well as potential recombination, was revealed among different CTV isolates. Five pure SP severe and two pure mild strains were identified by genotype composition analysis. Taken together, the results update the genetic diversity of CTV in Hunan with the detection of one possible novel strain, and this information might be applicable for the selection of appropriate mild CTV strains for controlling citrus SP disease through cross-protection.

Prevalence and characterization of Campylobacter jejuni isolated from pasture flock poultry.

Science.gov (United States)

Hanning, Irene; Biswas, Debabrata; Herrera, Paul; Roesler, Mary; Ricke, Steven C

2010-09-01

The growing interest in organic and natural foods warrants a greater need for information on the food safety of these products. In this study, samples were taken from 2 pasture flock farms (N = 178; feed, water, drag swabs, and insect traps), pasture flock retail carcasses (N = 48) and 1 pasture flock processing facility (N = 16) over a period of 8 mo. A total of 105 Campylobacter isolates were obtained from 53 (30%), 36 (75%), and 16 (100%) samples from the farms, retail carcasses, and processing facility, respectively. Of the 105 isolates collected, 65 were C. jejuni, 31 were C. coli, and 9 were other Campylobacter spp. Using PCR, the C. jejuni isolates were further analyzed for virulence genes involved in colonization and survival (flaA, flaC, cadF, dnaJ, racR, cbrR), invasion (virB11, ciaB, pldA), protection against harsh conditions (sodB, htrA, clpA), toxin production (cdtA, cdtB, cdtC), siderophore transport (ceuE), and ganglioside mimicry (wlaN). In addition, the short variable region of the flaA locus (flaA SVR) was sequenced to determine the genetic diversity of the C. jejuni isolates. The flaA SVR diversity indices increased along the farm to carcass continuum. PCR-based analysis indicated a low prevalence of 5 genes involved in colonization (dnaJ, ciaB, pldA, racR, virB11). The results of this survey indicate that the prevalence of Campylobacter on organic retail carcasses is similar to prevalence reports of Campylobacter on conventional retail carcasses. However, the genetic diversity of the flaA SVR genotypes increased along the farm to carcass continuum that contrasted with conventional poultry studies. Campylobacter jejuni is a leading cause of foodborne illness with poultry and poultry products being leading sources of infection. Free-range and pasture flock chickens are becoming more popular; however, there is an inherent biosecurity risk that can increase the prevalence of foodborne pathogens in these flocks. This study aimed to determine sources

Diversity of soil fungi in North 24 Parganas and their antagonistic potential against Leucinodes orbonalis Guen. (Shoot and fruit borer of brinjal).

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Pal, Sujoy; Ghosh, Swapan Kumar

2014-12-01

Soil samples were collected from agricultural fields and gardens in North 24 Parganas, West Bengal, and fungi species were isolated from them. Thirty-one fungal species were isolated with 19 found in agricultural soil and 28 in garden soil. Twenty-eight out of 31 were identified using cultural and microscopic characters, and three were unidentified. The diversity of isolated fungi was calculated by Simpson's diversity index. The garden soil possessed more fungal colonies (750) than agricultural soil (477). In agricultural soil, the dominant fungi were Aspergillus niger, Rhizopus oryzae, and Penicillium expansum, and the dominant fungi of garden soil were A. niger and Fusarium moniliforme. Simpson's diversity index indicated that garden soil had more fungal diversity (0.939) than agricultural soil (0.896). The entomopathogenic capacity of the isolated fungi was tested against the brinjal shoot and fruit borer (Leucinodes orbonalis Guen) which is the major insect pest of brinjal. The isolated fungi were screened against larva of L. orbonalis for their entomopathogenic potential. Beauveria bassiana, A. niger, and P. expansum showed appreciable antagonism to L. orbonalis, and their lethal doses with 50 % mortality (LD50s) were 4.0 × 10(7), 9.06 × 10(7), and 1.50 × 10(8) spore/mL, respectively, and their times taken to reach 50 % mortality (LT50s) were 9.77, 10.56, and 10.60 days, respectively. This work suggests the restriction of chemical pesticide application in agricultural fields to increase fungal diversity. The entomopathogenic efficacy of B. bassiana could be used in agricultural fields to increase fugal diversity and protect the brinjal crop.

Genetic diversity of Mycobacterium tuberculosis isolates from central India

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Prabha Desikan

2016-01-01

Interpretation & conclusions: Well established SITs were found to be predominant in our study. SIT26/CAS1_DEL was the most predominant type. However, the occurrence of a substantial number of orphan isolates may indicate the presence of active spatial and temporal evolutionary dynamics within the isolates of M. tuberculosis.

Diversity of Staphylococcus aureus Isolates in European Wildlife.

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Stefan Monecke

Full Text Available Staphylococcus aureus is a well-known colonizer and cause of infection among animals and it has been described from numerous domestic and wild animal species. The aim of the present study was to investigate the molecular epidemiology of S. aureus in a convenience sample of European wildlife and to review what previously has been observed in the subject field. 124 S. aureus isolates were collected from wildlife in Germany, Austria and Sweden; they were characterized by DNA microarray hybridization and, for isolates with novel hybridization patterns, by multilocus sequence typing (MLST. The isolates were assigned to 29 clonal complexes and singleton sequence types (CC1, CC5, CC6, CC7, CC8, CC9, CC12, CC15, CC22, CC25, CC30, CC49, CC59, CC88, CC97, CC130, CC133, CC398, ST425, CC599, CC692, CC707, ST890, CC1956, ST2425, CC2671, ST2691, CC2767 and ST2963, some of which (ST2425, ST2691, ST2963 were not described previously. Resistance rates in wildlife strains were rather low and mecA-MRSA isolates were rare (n = 6. mecC-MRSA (n = 8 were identified from a fox, a fallow deer, hares and hedgehogs. The common cattle-associated lineages CC479 and CC705 were not detected in wildlife in the present study while, in contrast, a third common cattle lineage, CC97, was found to be common among cervids. No Staphylococcus argenteus or Staphylococcus schweitzeri-like isolates were found. Systematic studies are required to monitor the possible transmission of human- and livestock-associated S. aureus/MRSA to wildlife and vice versa as well as the possible transmission, by unprotected contact to animals. The prevalence of S. aureus/MRSA in wildlife as well as its population structures in different wildlife host species warrants further investigation.

Bullying in an Increasingly Diverse School Population: A Socio-Ecological Model Analysis

Science.gov (United States)

Lim, Seok Jeng Jane; Hoot, James L.

2015-01-01

Systematic research into bullying has a short history spanning about 40 years. However, investigations into school bullying from a multicultural context are especially limited. As schools in the 21st century become increasingly diverse due to rapid globalization and immigration, there is a need to consider bullying within changing populations. The…

An Evaluation of the Genetic Diversity of Xylella fastidiosa Isolated from Diseased Citrus and Coffee in São Paulo, Brazil.

Science.gov (United States)

Qin, X; Miranda, V S; Machado, M A; Lemos, E G; Hartung, J S

2001-06-01

ABSTRACT Strains of Xylella fastidiosa, isolated from sweet orange trees (Citrus sinensis) and coffee trees (Coffea arabica) with symptoms of citrus variegated chlorosis and Requeima do Café, respectively, were indistinguishable based on repetitive extragenic palindromic polymerase chain reaction (PCR) and enterobacterial repetitive intergenic consensus PCR assays. These strains were also indistinguishable with a previously described PCR assay that distinguished the citrus strains from all other strains of Xylella fastidiosa. Because we were not able to document any genomic diversity in our collection of Xylella fastidiosa strains isolated from diseased citrus, the observed gradient of increasing disease severity from southern to northern regions of São Paulo State is unlikely due to the presence of significantly different strains of the pathogen in the different regions. When comparisons were made to reference strains of Xylella fastidiosa isolated from other hosts using these methods, four groups were consistently identified consistent with the hosts and regions from which the strains originated: citrus and coffee, grapevine and almond, mulberry, and elm, plum, and oak. Independent results from random amplified polymorphic DNA (RAPD) PCR assays were also consistent with these results; however, two of the primers tested in RAPD-PCR were able to distinguish the coffee and citrus strains. Sequence comparisons of a PCR product amplified from all strains of Xylella fastidiosa confirmed the presence of a CfoI polymorphism that can be used to distinguish the citrus strains from all others. The ability to distinguish Xylella fastidiosa strains from citrus and coffee with a PCR-based assay will be useful in epidemiological and etiological studies of this pathogen.

Trichothecene chemotype diversity of Fusarium graminearum isolated from wheat, maize and barley in Serbia

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Obradović Ana

2017-01-01

Full Text Available Diversity of trichothecene chemotypes of Fusarium graminearum isolated from kernels of wheat, barley and maize grown under various agro-ecological conditions on 13 locations was analysed. Sixteen strains were tested for the effective capability to produce 15-ADON, 3-ADON and NIV, by using the liquid chromatography-tandem mass spectrometry (LC-MS/MS system. Fourteen out of sixteen analyzed strains produced 15-ADON, while remaining two were of the 3-ADON chemotype. Multiplex PCR reaction with two sets of specific primers for TRI3 and TRI12 genes was applied to identify trichothecene chemotypes (3-ADON, 15-ADON and NIV. The expected sizes of amplified fragments for TRI3 gene primer set are 840 bp (NIV, 610 bp (15-ADON and 243 bp (3-ADON. The amplified fragments for TRI12 gene primer set should be 840 bp (NIV, 670 bp (15-ADON and 410 bp (3-ADON. All F. graminearum isolates were of the 15-ADON chemotype, i.e. their bands were 610 bp and 670 bp size for TRI3 and TRI12 genes, respectively. The results indicate that genotypic characterisation does not correspond to determined chemotypes and this is a reason why the analyses for the risk of mycotoxins contamination should not be based only on trichotecene genotype determination. Due to high temperature differences in cereal growing regions in Serbia, the presence of other chemotypes could be expected. In order to determine whether besides 15-ADON there are other F. graminearum chemotypes on wheat, barley and maize kernels, further studies should include a large number of isolates from different agro-ecological conditions. [Project of the Serbian Ministry of Education, Science and Technological Development, Grant no. TR31023

Identification and characterization of psychrotolerant coliform bacteria isolated from pasteurized fluid milk.

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Masiello, S N; Martin, N H; Trmčić, A; Wiedmann, M; Boor, K J

2016-01-01

The presence of coliform bacteria in pasteurized fluid milk typically indicates that product contamination occurred downstream of the pasteurizer, but it may also indicate pasteurization failure. Although coliform detection is frequently used as a hygiene indicator for dairy products, our understanding of the taxonomic and phenotypic coliform diversity associated with dairy products is surprisingly limited. Therefore, using Petrifilm Coliform Count plates (3M, St. Paul, MN), we isolated coliforms from high-temperature, short-time (HTST)-pasteurized fluid milk samples from 21 fluid milk processing plants in the northeast United States. Based on source information and initial characterization using partial 16S rDNA sequencing, 240 nonredundant isolates were obtained. The majority of these isolates were identified as belonging to the genera Enterobacter (42% of isolates), Hafnia (13%), Citrobacter (12%), Serratia (10%), and Raoultella (9%); additional isolates were classified into the genera Buttiauxella, Cedecea, Kluyvera, Leclercia, Pantoea, and Rahnella. A subset of 104 representative isolates was subsequently characterized phenotypically. Cold growth analysis in skim milk broth showed that all isolates displayed at least a 2-log increase over 10 d at 6°C; the majority of isolates (n=74) displayed more than a 5-log increase. In total, 43% of the representative isolates displayed lipolysis when incubated on spirit blue agar at 6°C for 14 d, whereas 71% of isolates displayed proteolysis when incubated on skim milk agar at 6°C for 14 d. Our data indicate that a considerable diversity of coliforms is found in HTST-pasteurized fluid milk and that a considerable proportion of these coliforms have phenotypic characteristics that will allow them to cause fluid milk spoilage. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

[Diversity of cultivable actinobacteria in Xinghu wetland sediments].

Science.gov (United States)

Xue, Dong; Zhao, Guozhen; Yao, Qing; Zhao, Haiquan; Zhu, Honghui

2015-11-04

To study the diversity of cultivable actinobacteria in Xinghu wetland and screen actinobacteria with a pharmaceutical potential for producing biologically active secondary metabolites. We studied the diversity of actinobacteria isolated from Xinghu wetland by using different selective isolation media and methods. The high bioactive actinobacteria were identified and further investigated for the presence of polyketide synthases (PKS-I, PKS-II), nonribosomal peptide synthetases (NRPS), 3-amino-5-hydroxybenzoic acid synthases (AHBA) and 3-hydroxy-3-methylglutaryl Coenzyme A (HMG CoA) sequences by specific amplification. More than 300 actinobacteria were isolated, and 135 isolates were selected on the basis of their morphologies on different media and were further characterized by 16S rRNA gene sequencing. The isolates belonged to 7 orders, 10 families, 13 genera, Streptomyces was the most frequently isolated genus, followed by the genera Micromonospora and Nocardia. Twenty-four isolates showed high activity against Staphylococcus aureus and Escherichia coli, but there no strain displaying antagonistic activity against Salmonella sp. High frequencies of positive PCR amplification were obtained for PKS-I (16.7%, 4/24), PKS-II (62.5%,15/24), NRPS (16.7%, 4/24), HMG CoA (29.2%, 7/24) and AHBA (12.5%, 3/24) biosynthetic systems. High Performance Liquid Chromatography showed that strain XD7, XD114, XD128 produce lots of secondary metabolites. This study indicated that actinobacteria isolated from Xinghu wetland are abundant and have potentially beneficial and diverse bioactivities which should be pursued for their biotechnical promise.

Strategic Design of Synthetic Consortium with embedded Wastewater Treatment Potential: Deciphering the Competence of Isolates from Diverse Microbiome

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Shikha eDahiya

2016-05-01

Full Text Available Microorganisms plays vital role in efficient biological treatment. Supplementation of external microorganisms with high degradation rates can enhance the process efficiency significantly. Potential strains were isolated from long term wastewater treating reactors and identified using phylogenetic analysis of 16S rRNA gene fragments with the nearest neighbours extracted during BLAST search. Later the study was designed in two phases which revealed interesting findings. Phase I evaluates the potential of isolated strains viz., Pseudomonas otitidis, Bacillus firmus, Bacillus subtilis and Bacillus circulans for their individual ability in terms of COD and nutrients removal. Bacillus circulans showed highest carbon (COD removal (70%; 0.56 kg CODR/m3-day, while maximum nutrients removal (nitrate, 81%; phosphates, 90% was observed with Bacillus subtilis. B. firmus showed maximum volatile fatty acid (VFA production. Based on Phase I results, four synthetic consortia were designed in phase II with diverse combination of isolates and evaluated for its remediation efficiencies. Consortium 4 (P. otitidis, B. subtilis and B. firmus illustrated higher treatment potential [COD, 86%; SDR (cum: 0.64 kg CODR/m3-day; Nitrates, 87%; Phosphates, 97%]. The exploitation of such explicit consortia can overcome the inefficiencies pre-existing with the biological wastewater treatment plants by acting as prospective candidates for bio-augmenting the native microflora. This communication illustrated development of the efficient consortia using lab isolated strains to improve the performance of wastewater treatment.

Genetic diversity of Colletotrichum gloeosporioides in Nigeria using ...

African Journals Online (AJOL)

fmodupe

2012-04-24

Apr 24, 2012 ... gloeosporioides isolates and was effective in establishing genetic relationships ... Key words: Anthracnose disease, pathotypes, genetic diversity, amplified ..... isolates to use in an anthracnose resistance screening program.

Molecular diversity of Rice grassy stunt virus in Vietnam.

Science.gov (United States)

Ta, Hoang-Anh; Nguyen, Doan-Phuong; Causse, Sandrine; Nguyen, Thanh-Duc; Ngo, Vinh-Vien; Hébrard, Eugénie

2013-04-01

Rice grassy stunt virus (RGSV, Tenuivirus) recently emerged on rice in Vietnam, causing high yield losses during 2006-2009. The genetic diversity of RGSV is poorly documented. In this study, the two genes encoded by each ambisense segment RNA3 and RNA5 of RGSV isolates from six provinces of South Vietnam were sequenced. P3 and Pc3 (RNA3) have unknown function, P5 (RNA5) encodes the putative silencing suppressor, and Pc5 (RNA5) encodes the nucleocapsid protein (N). The sequences of 17 Vietnamese isolates were compared with reference isolates from North and South Philippines. The average nucleotide diversity among the isolates was low. We confirmed a higher variability of RNA3 than RNA5 and Pc3 than P3. No relationships between the genetic diversity and the geographic distribution of RGSV isolates could be ascertained, likely because of the long-distance migration of the insect vector. This data will contribute to a better understanding on the RGSV epidemiology in South Vietnam, a prerequisite for further management of the disease and rice breeding for resistance.

Repeated burning of eastern tallgrass prairie increases richness and diversity, stabilizing late successional vegetation.

Science.gov (United States)

Bowles, Marlin L; Jones, Michael D

2013-03-01

Understanding temporal effects of fire frequency on plant species diversity and vegetation structure is critical for managing tallgrass prairie (TGP), which occupies a mid-continental longitudinal precipitation and productivity gradient. Eastern TGP has contributed little information toward understanding whether vegetation-fire interactions are uniform or change across this biome. We resampled 34 fire-managed mid- and late-successional ungrazed TGP remnants occurring across a dry to wet-mesic moisture gradient in the Chicago region of Illinois, USA. We compared hypotheses that burning acts either as a stabilizing force or causes change in diversity and structure, depending upon fire frequency and successional stage. Based on western TGP, we expected a unimodal species richness distribution across a cover-productivity gradient, variable functional group responses to fire frequency, and a negative relationship between fire frequency and species richness. Species diversity was unimodal across the cover gradient and was more strongly humpbacked in stands with greater fire frequency. In support of a stabilizing hypothesis, temporal similarity of late-successional vegetation had a logarithmic relationship with increasing fire frequency, while richness and evenness remained stable. Temporal similarity within mid-successional stands was not correlated with fire frequency, while richness increased and evenness decreased over time. Functional group responses to fire frequency were variable. Summer forb richness increased under high fire frequency, while C4 grasses, spring forbs, and nitrogen-fixing species decreased with fire exclusion. On mesic and wet-mesic sites, vegetation structure measured by the ratio of woody to graminoid species was negatively correlated with abundance of forbs and with fire frequency. Our findings that species richness responds unimodally to an environmental-productivity gradient, and that fire exclusion increases woody vegetation and leads to loss

Preoperative Aspirin Does Not Increase Transfusion or Reoperation in Isolated Valve Surgery.

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Goldhammer, Jordan E; Herman, Corey R; Berguson, Mark W; Torjman, Marc C; Epstein, Richard H; Sun, Jian-Zhong

2017-10-01

Preoperative aspirin has been studied in patients undergoing isolated coronary artery bypass graft surgery. However, there is a paucity of clinical data available evaluating perioperative aspirin in other cardiac surgical procedures. This study was designed to investigate the effects of aspirin on bleeding and transfusion in patients undergoing non-emergent, isolated, heart valve repair or replacement. Retrospective, cohort study. Academic medical center. A total of 694 consecutive patients having non-emergent, isolated, valve repair or replacement surgery at an academic medical center were identified. Of the 488 patients who met inclusion criteria, 2 groups were defined based on their preoperative use of aspirin: those taking (n = 282), and those not taking (n = 206) aspirin within 5 days of surgery. Binary logistic regression was used to examine relationships among demographic and clinical variables. No significant difference was found between the aspirin and non-aspirin groups with respect to the percentage receiving red blood cell (RBC) transfusion, mean RBC units transfused in those who required transfusion, massive transfusion of RBC, or amounts of fresh frozen plasma, cryoprecipitate, or platelets. Aspirin was not associated with an increase in the rate of re-exploration for bleeding (5.3% v 6.3%, p = 0.478). Major adverse cardiocerebral events (MACE), 30-day mortality, and 30-day readmission rates were not statistically different between the aspirin-and non-aspirin-treated groups. Preoperative aspirin therapy in elective, isolated, valve surgery did not result in an increase in transfusion or reoperation for bleeding and was not associated with reduced readmission rate, MACE, or 30-day mortality. Copyright © 2017 Elsevier Inc. All rights reserved.

Dr. Stefan Ambs: Increasing Diversity in Cancer Research: One Lab at a Time

Science.gov (United States)

As part of the series “Increasing Diversity in Cancer Research,” CRCHD interviewed Dr. Stefan Ambs, an investigator at NCI’s Center for Cancer Research, who is using novel approaches to discover gene differences in the tumors of African American patients.

The Diversity of the Limnohabitans Genus, an Important Group of Freshwater Bacterioplankton, by Characterization of 35 Isolated Strains

Science.gov (United States)

Kasalický, Vojtěch; Jezbera, Jan; Hahn, Martin W.; Šimek, Karel

2013-01-01

Bacteria of the genus Limnohabitans, more precisely the R-BT lineage, have a prominent role in freshwater bacterioplankton communities due to their high rates of substrate uptake and growth, growth on algal-derived substrates and high mortality rates from bacterivory. Moreover, due to their generally larger mean cell volume, compared to typical bacterioplankton cells, they contribute over-proportionally to total bacterioplankton biomass. Here we present genetic, morphological and ecophysiological properties of 35 bacterial strains affiliated with the Limnohabitans genus newly isolated from 11 non-acidic European freshwater habitats. The low genetic diversity indicated by the previous studies using the ribosomal SSU gene highly contrasted with the surprisingly rich morphologies and different patterns in substrate utilization of isolated strains. Therefore, the intergenic spacer between 16S and 23S rRNA genes was successfully tested as a fine-scale marker to delineate individual lineages and even genotypes. For further studies, we propose the division of the Limnohabitans genus into five lineages (provisionally named as LimA, LimB, LimC, LimD and LimE) and also additional sublineages within the most diversified lineage LimC. Such a delineation is supported by the morphology of isolated strains which predetermine large differences in their ecology. PMID:23505469

Genetic diversity and antibiogram profile of diarrhoeagenic Escherichia coli pathotypes isolated from human, animal, foods and associated environmental sources

Directory of Open Access Journals (Sweden)

Pankaj Dhaka

2016-05-01

Full Text Available Introduction: Infectious diarrhoea particularly due to pathogenic bacteria is a major health problem in developing countries, including India. Despite significant reports of diarrhoeagenic Escherichia coli (DEC pathotypes around the globe, studies which address genetic relatedness, antibiogram profile and their correlation with respect to their isolation from different sources are sparse. The present study determines isolation and identification of DEC pathotypes from different sources, their genetic characterisation, antibiogram profile and their correlation if any. Materials and methods: A total of 336 samples comprising diarrhoeic stool samples from infants (n=103, young animal (n=106, foods (n=68 and associated environmental sources (n=59 were collected from Bareilly region of India. All the samples were screened by using standard microbiological methods for the detection of E. coli. The identified E. coli were then confirmed as DEC pathotypes using polymerase chain reaction–based assays. Those DEC pathotypes identified as Enteroaggregative E. coli (EAEC were further confirmed using HEp-2 adherence assay. All the isolated DEC pathotypes were studied for their genetic diversity using pulsed-field gel electrophoresis (PFGE, and antimicrobial susceptibility testing was performed by using disc diffusion method as per Clinical Laboratory Standards Institute guidelines. Results and discussion: Of the four DEC pathotypes investigated, EAEC was found to be the predominant pathogen with an isolation rate of 16.5% from infants, 17.9% from young animals, 16.2% from foods and 3.4% from the associated environmental sources. These EAEC isolates, on further characterisation, revealed predominance of ‘atypical’ EAEC, with an isolation rate of 10.7% from infants, 15.1% from young animals, 16.2% from foods, and 3.4% from the associated environmental sources. On PFGE analysis, discrimination was evident within DEC pathotypes as 52 unique pulsotypes were

Pulsed-field profile diversities of Salmonella Enteritidis, S. Infantis, and S. Corvallis in Japan

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Koichi Murakami

2017-10-01

Full Text Available The diversity of pulsed-field profiles (PFPs within non-typhoidal Salmonella subtypes influences epidemiological analyses of Salmonella outbreaks. Therefore, determining the PFP diversity of each Salmonella serovar is important when evaluating current circulating strains. This study examined the PFP diversity of three important public health Salmonella enterica subspecies enterica serovars, S. Enteritidis (n=177, S. Infantis (n=205, and S. Corvallis (n=90, using pulsed-field gel electrophoresis. Isolates were collected from several sources, primarily from chicken-derived samples, in the Kyushu-Okinawa region of Japan between 1989 and 2005. S. Enteritidis isolates displayed 51 distinct PFPs (E-PFPs, with 92 (52.0% and 32 (18.1% isolates displaying types EPFP1 and E-PFP10, respectively. The 205 S. Infantis isolates showed 54 distinct PFPs (I-PFPs, with 87 (42.4% and 36 (17.6% isolates being I-PFP4 and I-PFP2, respectively. I-PFP18 was the dominant I-PFP of layer chicken isolates across a 5-year period. Fourteen distinct S. Corvallis PFPs were detected. Simpson’s index results for the genetic diversities of S. Enteritidis, S. Infantis, and S. Corvallis isolates were 0.70, 0.79, and 0.78, respectively. None of the EPFPs or I-PFPs of layer chicken isolates overlapped with those of broiler chicken isolates, and the dominant clonal lines existed for >10 years. In conclusion, limited PFP diversities were detected amongst S. Enteritidis, S. Infantis, and S. Corvallis isolates of primarily chicken-derived origins in the Kyushu-Okinawa region of Japan. Therefore, it is important to take into account these limitations in PFP diversities in epidemiological analyses of Salmonella outbreaks.

Pulsed-field profile diversities of Salmonella Enteritidis, S. Infantis, and S. Corvallis in Japan.

Science.gov (United States)

Murakami, Koichi; Noda, Tamie; Onozuka, Daisuke; Kimura, Hirokazu; Fujimoto, Shuji

2017-08-16

The diversity of pulsed-field profiles (PFPs) within non-typhoidal Salmonella subtypes influences epidemiological analyses of Salmonella outbreaks. Therefore, determining the PFP diversity of each Salmonella serovar is important when evaluating current circulating strains. This study examined the PFP diversity of three important public health Salmonella enterica subspecies enterica serovars, S . Enteritidis (n=177), S . Infantis (n=205), and S . Corvallis (n=90), using pulsed-field gel electrophoresis. Isolates were collected from several sources, primarily from chicken-derived samples, in the Kyushu-Okinawa region of Japan between 1989 and 2005. S . Enteritidis isolates displayed 51 distinct PFPs (E-PFPs), with 92 (52.0%) and 32 (18.1%) isolates displaying types E-PFP1 and E-PFP10, respectively. The 205 S . Infantis isolates showed 54 distinct PFPs (I-PFPs), with 87 (42.4%) and 36 (17.6%) isolates being I-PFP4 and I-PFP2, respectively. I-PFP18 was the dominant I-PFP of layer chicken isolates across a 5-year period. Fourteen distinct S . Corvallis PFPs were detected. Simpson's index results for the genetic diversities of S . Enteritidis, S . Infantis, and S . Corvallis isolates were 0.70, 0.79, and 0.78, respectively. None of the E-PFPs or I-PFPs of layer chicken isolates overlapped with those of broiler chicken isolates, and the dominant clonal lines existed for >10 years. In conclusion, limited PFP diversities were detected amongst S . Enteritidis, S. Infantis, and S. Corvallis isolates of primarily chicken-derived origins in the Kyushu-Okinawa region of Japan. Therefore, it is important to take into account these limitations in PFP diversities in epidemiological analyses of Salmonella outbreaks.

Increasing plant diversity with border crops reduces insecticide use and increases crop yield in urban agriculture.

Science.gov (United States)

Wan, Nian-Feng; Cai, You-Ming; Shen, Yan-Jun; Ji, Xiang-Yun; Wu, Xiang-Wen; Zheng, Xiang-Rong; Cheng, Wei; Li, Jun; Jiang, Yao-Pei; Chen, Xin; Weiner, Jacob; Jiang, Jie-Xian; Nie, Ming; Ju, Rui-Ting; Yuan, Tao; Tang, Jian-Jun; Tian, Wei-Dong; Zhang, Hao; Li, Bo

2018-05-24

Urban agriculture is making an increasing contribution to food security in large cities around the world. The potential contribution of biodiversity to ecological intensification in urban agricultural systems has not been investigated. We present monitoring data collected from rice fields in 34 community farms in mega-urban Shanghai, China, from 2001 to 2015, and show that the presence of a border crop of soybeans and neighboring crops (maize, eggplant and Chinese cabbage), both without weed control, increased invertebrate predator abundance, decreased the abundance of pests and dependence on insecticides, and increased grain yield and economic profits. Two 2 year randomized experiments with the low and high diversity practices in the same locations confirmed these results. Our study shows that diversifying farming practices can make an important contribution to ecological intensification and the sustainable use of associated ecosystem services in an urban ecosystem. © 2018, Wan et al.

Characterization of bacterial diversity associated with calcareous deposits and drip-waters, and isolation of calcifying bacteria from two Colombian mines.

Science.gov (United States)

García G, Mariandrea; Márquez G, Marco Antonio; Moreno H, Claudia Ximena

2016-01-01

Bacterial carbonate precipitation has implications in geological processes and important biotechnological applications. Bacteria capable of precipitating carbonates have been isolated from different calcium carbonate deposits (speleothems) in caves, soil, freshwater and seawater around the world. However, the diversity of bacteria from calcareous deposits in Colombia, and their ability to precipitate carbonates, remains unknown. In this study, conventional microbiological methods and molecular tools, such as temporal temperature gradient electrophoresis (TTGE), were used to assess the composition of bacterial communities associated with carbonate deposits and drip-waters from two Colombian mines. A genetic analysis of these bacterial communities revealed a similar level of diversity, based on the number of bands detected using TTGE. The dominant phylogenetic affiliations of the bacteria, determined using 16S rRNA gene sequencing, were grouped into two phyla: Proteobacteria and Firmicutes. Within these phyla, seven genera were capable of precipitating calcium carbonates: Lysinibacillus, Bacillus, Strenotophomonas, Brevibacillus, Methylobacterium, Aeromicrobium and Acinetobacter. FTIR and SEM/EDX were used to analyze calcium carbonate crystals produced by isolated Acinetobacter gyllenbergii. The results showed that rhombohedral and angular calcite crystals with sizes of 90μm were precipitated. This research provides information regarding the presence of complex bacterial communities in secondary carbonate deposits from mines and their ability to precipitate calcium carbonate from calcareous deposits of Colombian mines. Copyright © 2015 Elsevier GmbH. All rights reserved.

Lysogenic Streptococcus suis isolate SS2-4 containing prophage SMP showed increased mortality in zebra fish compared to the wild-type isolate.

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Fang Tang

Full Text Available Streptococcus suis (S. suis infection is considered to be a major problem in the swine industry worldwide. Based on the capsular type, 33 serotypes of S. suis have been described, with serotype 2 (SS2 being the most frequently isolated from diseased piglets. Little is known, however, about the pathogenesis and virulence factors of S. suis. Research on bacteriophages highlights a new area in S. suis research. A S. suis serotype 2 bacteriophage, designated SMP, has been previously isolated in our laboratory. Here, we selected a lysogenic isolate in which the SMP phage was integrated into the chromosome of strain SS2-4. Compared to the wild-type isolate, the lysogenic strain showed increased mortality in zebra fish. Moreover the sensitivity of the lysogenic strain to lysozyme was seven times higher than that of the wild-type.

Genetic diversity of Plasmodium vivax and Plasmodium falciparum in Honduras.

Science.gov (United States)

Lopez, Ana Cecilia; Ortiz, Andres; Coello, Jorge; Sosa-Ochoa, Wilfredo; Torres, Rosa E Mejia; Banegas, Engels I; Jovel, Irina; Fontecha, Gustavo A

2012-11-26

Understanding the population structure of Plasmodium species through genetic diversity studies can assist in the design of more effective malaria control strategies, particularly in vaccine development. Central America is an area where malaria is a public health problem, but little is known about the genetic diversity of the parasite's circulating species. This study aimed to investigate the allelic frequency and molecular diversity of five surface antigens in field isolates from Honduras. Five molecular markers were analysed to determine the genotypes of Plasmodium vivax and Plasmodium falciparum from endemic areas in Honduras. Genetic diversity of ama-1, msp-1 and csp was investigated for P. vivax, and msp-1 and msp-2 for P. falciparum. Allelic frequencies were calculated and sequence analysis performed. A high genetic diversity was observed within Plasmodium isolates from Honduras. A different number of genotypes were elucidated: 41 (n = 77) for pvama-1; 23 (n = 84) for pvcsp; and 23 (n = 35) for pfmsp-1. Pvcsp sequences showed VK210 as the only subtype present in Honduran isolates. Pvmsp-1 (F2) was the most polymorphic marker for P. vivax isolates while pvama-1 was least variable. All three allelic families described for pfmsp-1 (n = 30) block 2 (K1, MAD20, and RO33), and both allelic families described for the central domain of pfmsp-2 (n = 11) (3D7 and FC27) were detected. However, K1 and 3D7 allelic families were predominant. All markers were randomly distributed across the country and no geographic correlation was found. To date, this is the most complete report on molecular characterization of P. vivax and P. falciparum field isolates in Honduras with regards to genetic diversity. These results indicate that P. vivax and P. falciparum parasite populations are highly diverse in Honduras despite the low level of transmission.

The implementation of base isolation in the United States

International Nuclear Information System (INIS)

Kelly, J.M.

1993-01-01

The concept of base isolation as an innovative means of providing earthquake resistance to structural systems was met initially with a great deal of skepticism by the engineering community. Today, however, it is on the cutting edge of seismic-resistance engineering, as evidenced by the rapidly increasing number of buildings, both new construction and retrofit, using this earthquake-resistant technique. It is now generally accepted that a base-isolated building will perform better than a conventional fixed-base building in moderate or strong earthquakes. In the structures in which it has been used so far, the major benefit has been to reduce the effects of seismic forces on contents and internal equipment, more than justifying the increased cost of isolated construction. This review will mainly cover the development and application of base isolation to buildings in the US. The acceptance of this approach has been slow, but as a result of the 1989 Loma Prieta earthquake there is an increasing interest in its use for repair of buildings damaged in that earthquake and for the retrofit of historic buildings that are considered vulnerable to earthquake loading. Base isolation may play a major role in the future in projects as diverse as advanced nuclear reactors and public housing in developing countries

A Systematic Review: The Next Generation Science Standards and the Increased Cultural Diversity

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Asowayan, Alaa A.; Ashreef, Samaar Y.; Omar, Sozan H.

2017-01-01

This systematic review aims to explore the effect of NGSS on students' academic excellence. Specifically, considering increased cultural diversity, it is appropriate to identify student's science-related values, respectful features of teachers' cultural competence, and underlying challenges and detect in what ways these objectives are addressed by…

Effects of local tree diversity on herbivore communities diminish with increasing forest fragmentation on the landscape scale.

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Franziska Peter

Full Text Available Forest fragmentation and plant diversity have been shown to play a crucial role for herbivorous insects (herbivores, hereafter. In turn, herbivory-induced leaf area loss is known to have direct implications for plant growth and reproduction as well as long-term consequences for ecosystem functioning and forest regeneration. So far, previous studies determined diverging responses of herbivores to forest fragmentation and plant diversity. Those inconsistent results may be owed to complex interactive effects of both co-occurring environmental factors albeit they act on different spatial scales. In this study, we investigated whether forest fragmentation on the landscape scale and tree diversity on the local habitat scale show interactive effects on the herbivore community and leaf area loss in subtropical forests in South Africa. We applied standardized beating samples and a community-based approach to estimate changes in herbivore community composition, herbivore abundance, and the effective number of herbivore species on the tree species-level. We further monitored leaf area loss to link changes in the herbivore community to the associated process of herbivory. Forest fragmentation and tree diversity interactively affected the herbivore community composition, mainly by a species turnover within the family of Curculionidae. Furthermore, herbivore abundance increased and the number of herbivore species decreased with increasing tree diversity in slightly fragmented forests whereas the effects diminished with increasing forest fragmentation. Surprisingly, leaf area loss was neither affected by forest fragmentation or tree diversity, nor by changes in the herbivore community. Our study highlights the need to consider interactive effects of environmental changes across spatial scales in order to draw reliable conclusions for community and interaction patterns. Moreover, forest fragmentation seems to alter the effect of tree diversity on the herbivore

Diversity of plant oil seed-associated fungi isolated from seven oil-bearing seeds and their potential for the production of lipolytic enzymes.

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Venkatesagowda, Balaji; Ponugupaty, Ebenezer; Barbosa, Aneli M; Dekker, Robert F H

2012-01-01

Commercial oil-yielding seeds (castor, coconut, neem, peanut, pongamia, rubber and sesame) were collected from different places in the state of Tamil Nadu (India) from which 1279 endophytic fungi were isolated. The oil-bearing seeds exhibited rich fungal diversity. High Shannon-Index H' was observed with pongamia seeds (2.847) while a low Index occurred for coconut kernel-associated mycoflora (1.018). Maximum Colonization Frequency (%) was observed for Lasiodiplodia theobromae (176). Dominance Index (expressed in terms of the Simpson's Index D) was high (0.581) for coconut kernel-associated fungi, and low for pongamia seed-borne fungi. Species Richness (Chao) of the fungal isolates was high (47.09) in the case of neem seeds, and low (16.6) for peanut seeds. All 1279 fungal isolates were screened for lipolytic activity employing a zymogram method using Tween-20 in agar. Forty isolates showed strong lipolytic activity, and were morphologically identified as belonging to 19 taxa (Alternaria, Aspergillus, Chalaropsis, Cladosporium, Colletotrichum, Curvularia, Drechslera, Fusarium, Lasiodiplodia, Mucor, Penicillium, Pestalotiopsis, Phoma, Phomopsis, Phyllosticta, Rhizopus, Sclerotinia, Stachybotrys and Trichoderma). These isolates also exhibited amylolytic, proteolytic and cellulolytic activities. Five fungal isolates (Aspergillus niger, Chalaropsis thielavioides, Colletotrichum gloeosporioides, Lasiodiplodia theobromae and Phoma glomerata) exhibited highest lipase activities, and the best producer was Lasiodiplodia theobromae (108 U/mL), which was characterized by genomic sequence analysis of the ITS region of 18S rDNA.

Bovine viral diarrhea virus (BVDV genetic diversity in Spain: A review

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Francisco J. Diéguez

2017-07-01

Full Text Available Bovine viral diarrhea virus (BVDV, a member of the genus Pestivirus of the family Flaviviridae, causes significant losses in cattle farming worldwide because of reduced milk production, increased mortality of young animals and reproductive, respiratory and intestinal problems. The virus is characterized by an important genetic, and consequently antigenic and pathogenic diversity. Knowing the variability of viral strains present in a population provides valuable information, particularly relevant for control programs development, vaccination recommendations and even identification of likely infection sources. Such information is therefore important at both local and regional levels. This review focuses on the genetic diversity of BVDV isolates infecting cattle in Spain over the last years. According to the published data, the most prevalent BVDV group in Spain was 1b, and to a lesser extent 1d, 1e and 1f. Besides, BVDV-2 has also been found in Spain with several ratified isolates. The studies carried out in Spain also showed increased genetic heterogeneity of BVDV strains, possibly due to a more intensive use of analytical tools available, presenting studies with increasingly greater sample sizes.

Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment

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Collin M Timm

2015-10-01

Full Text Available The bacterial microbiota of plants is diverse, with 1,000s of operational taxonomic units (OTUs associated with any individual plant. In this work we investigate the differences between 19 sequenced Pseudomonas fluorescens strains, isolated from Populus deltoides rhizosphere and endosphere and which represent a single OTU, using phenotypic analysis, comparative genomics, and metabolic models. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for plant-bacterial interactions are enriched in endosphere isolate genomes. Further, growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased towards endosphere isolates. Endosphere isolates have significantly more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways representative of plant-bacterial interactions but show metabolic bias towards chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria and are enriched among closely related isolates.

Evaluation of mating type distribution and genetic diversity of three Magnaporthe oryzae avirulence genes, PWL-2, AVR-Pii and Avr-Piz-t, in Thailand rice blast isolates

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Thanyaluk Sirisathaworn

2017-02-01

Full Text Available Rice blast disease, caused by the filamentous ascomycete fungus Magnaporthe oryzae (anamorph Pyricularia oryzae, has been ranked among the most important diseases of rice. The molecular mechanisms against this fungus follow the idea of “gene-for-gene interaction”, in which a plant resistance (R gene product recognizes a fungal avirulence (Avr effector and triggers the defense response. However, the Avr genes have been shown to be rapidly evolving resulting in high levels of genetic diversity. This study investigated genetic diversity that is influenced by sexual recombination and mutation for the adaptation of rice blast fungus to overcome the defense response. Mating type distribution and the nucleotide sequence variation of three avirulence genes were evaluated—PWL-2, Avr-Pii and Avr-Piz-t. In total, 77 rice blast isolates collected from infected rice plants in northern, northeastern and central Thailand in 2005, 2010 and 2012, were used in the analysis with mating type and avirulence gene-specific primers. The results revealed that all the tested blast isolates belonged to the mating type MAT1-2, suggesting a lack of sexual recombination within the population. The successful rates of PWL-2, Avr-Pii and Avr-Piz-t gene-specific primer amplification were 100%, 60% and 54%, respectively. Base substitution mutation was observed in coding regions of the Avr-Pii and Avr-Piz-t genes. Although these results showed a low level of genetic diversity in Thai rice blast isolates, non-synonymous mutations did occur which revealed common mechanisms of selective pressure that are prone to adaptation of Avr genes. The information on nucleotide sequence variation and the genetic diversity of Avr genes obtained from this study could be useful for planning novel strategies in the development of rice breeding programs in Thailand.

Phenotype and envelope gene diversity of nef-deleted HIV-1 isolated from long-term survivors infected from a single source

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Sullivan John S

2007-07-01

Full Text Available Abstract Background The Sydney blood bank cohort (SBBC of long-term survivors consists of multiple individuals infected with attenuated, nef-deleted variants of human immunodeficiency virus type 1 (HIV-1 acquired from a single source. Long-term prospective studies have demonstrated that the SBBC now comprises slow progressors (SP as well as long-term nonprogressors (LTNP. Convergent evolution of nef sequences in SBBC SP and LTNP indicates the in vivo pathogenicity of HIV-1 in SBBC members is dictated by factors other than nef. To better understand mechanisms underlying the pathogenicity of nef-deleted HIV-1, we examined the phenotype and env sequence diversity of sequentially isolated viruses (n = 2 from 3 SBBC members. Results The viruses characterized here were isolated from two SP spanning a three or six year period during progressive HIV-1 infection (subjects D36 and C98, respectively and from a LTNP spanning a two year period during asymptomatic, nonprogressive infection (subject C18. Both isolates from D36 were R5X4 phenotype and, compared to control HIV-1 strains, replicated to low levels in peripheral blood mononuclear cells (PBMC. In contrast, both isolates from C98 and C18 were CCR5-restricted. Both viruses isolated from C98 replicated to barely detectable levels in PBMC, whereas both viruses isolated from C18 replicated to low levels, similar to those isolated from D36. Analysis of env by V1V2 and V3 heteroduplex tracking assay, V1V2 length polymorphisms, sequencing and phylogenetic analysis showed distinct intra- and inter-patient env evolution. Conclusion Independent evolution of env despite convergent evolution of nef may contribute to the in vivo pathogenicity of nef-deleted HIV-1 in SBBC members, which may not necessarily be associated with changes in replication capacity or viral coreceptor specificity.

Becoming Inclusive: A Code of Conduct for Inclusion and Diversity.

Science.gov (United States)

Schmidt, Bonnie J; MacWilliams, Brent R; Neal-Boylan, Leslie

There are increasing concerns about exclusionary behaviors and lack of diversity in the nursing profession. Exclusionary behaviors, which may include incivility, bullying, and workplace violence, discriminate and isolate individuals and groups who are different, whereas inclusive behaviors encourage diversity. To address inclusion and diversity in nursing, this article offers a code of conduct. This code of conduct builds on existing nursing codes of ethics and applies to nursing students and nurses in both educational and practice settings. Inclusive behaviors that are demonstrated in nurses' relationships with patients, colleagues, the profession, and society are described. This code of conduct provides a basis for measureable change, empowerment, and unification of the profession. Recommendations, implications, and a pledge to action are discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

Genetic and Toxigenic Variability within Aspergillus flavus Population Isolated from Maize in Two Diverse Environments in Kenya

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Sheila Okoth

2018-01-01

Full Text Available Aspergillus flavus is the main producer of carcinogenic aflatoxins in agricultural commodities such as maize. This fungus occurs naturally on crops, and produces aflatoxins when environmental conditions are favorable. The aim of this study is to analyse the genetic variability among 109 A. flavus isolates previously recovered from maize sampled from a known aflatoxin-hotspot (Eastern region, Kenya and the major maize-growing area in the Rift Valley (Kenya, and to determine their toxigenic potential. DNA analyses of internal transcribed spacer (ITS regions of ribosomal DNA, partial β-tubulin gene (benA and calmodulin gene (CaM sequences were used. The strains were further analyzed for the presence of four aflatoxin-biosynthesis genes in relation to their capability to produce aflatoxins and other metabolites, targeting the regulatory gene aflR and the structural genes aflP, aflD, and aflQ. In addition, the metabolic profile of the fungal strains was unraveled using state-of-the-art LC-MS/MS instrumentation. The three gene-sequence data grouped the isolates into two major clades, A. minisclerotigenes and A. flavus. A. minisclerotigenes was most prevalent in Eastern Kenya, while A. flavus was common in both regions. A. parasiticus was represented by a single isolate collected from Rift Valley. Diversity existed within the A. flavus population, which formed several subclades. An inconsistency in identification of some isolates using the three markers was observed. The calmodulin gene sequences showed wider variation of polymorphisms. The aflatoxin production pattern was not consistent with the presence of aflatoxigenic genes, suggesting an inability of the primers to always detect the genes or presence of genetic mutations. Significant variation was observed in toxin profiles of the isolates. This is the first time that a profound metabolic profiling of A. flavus isolates was done in Kenya. Positive associations were evident for some metabolites

Genetic and Toxigenic Variability within Aspergillus flavus Population Isolated from Maize in Two Diverse Environments in Kenya.

Science.gov (United States)

Okoth, Sheila; De Boevre, Marthe; Vidal, Arnau; Diana Di Mavungu, José; Landschoot, Sofie; Kyallo, Martina; Njuguna, Joyce; Harvey, Jagger; De Saeger, Sarah

2018-01-01

Aspergillus flavus is the main producer of carcinogenic aflatoxins in agricultural commodities such as maize. This fungus occurs naturally on crops, and produces aflatoxins when environmental conditions are favorable. The aim of this study is to analyse the genetic variability among 109 A. flavus isolates previously recovered from maize sampled from a known aflatoxin-hotspot (Eastern region, Kenya) and the major maize-growing area in the Rift Valley (Kenya), and to determine their toxigenic potential. DNA analyses of internal transcribed spacer (ITS) regions of ribosomal DNA, partial β-tubulin gene (benA) and calmodulin gene (CaM) sequences were used. The strains were further analyzed for the presence of four aflatoxin-biosynthesis genes in relation to their capability to produce aflatoxins and other metabolites, targeting the regulatory gene aflR and the structural genes aflP, aflD, and aflQ. In addition, the metabolic profile of the fungal strains was unraveled using state-of-the-art LC-MS/MS instrumentation. The three gene-sequence data grouped the isolates into two major clades, A. minisclerotigenes and A. flavus . A. minisclerotigenes was most prevalent in Eastern Kenya, while A. flavus was common in both regions. A. parasiticus was represented by a single isolate collected from Rift Valley. Diversity existed within the A. flavus population, which formed several subclades. An inconsistency in identification of some isolates using the three markers was observed. The calmodulin gene sequences showed wider variation of polymorphisms. The aflatoxin production pattern was not consistent with the presence of aflatoxigenic genes, suggesting an inability of the primers to always detect the genes or presence of genetic mutations. Significant variation was observed in toxin profiles of the isolates. This is the first time that a profound metabolic profiling of A. flavus isolates was done in Kenya. Positive associations were evident for some metabolites, while for

Trust in a Time of Increasing Diversity

DEFF Research Database (Denmark)

Dinesen, Peter Thisted; Sønderskov, Kim Mannemar

2012-01-01

. Existing evidence from the Anglo-Saxon countries would suggest that this is the case, whereas evidence from the European continent mainly suggests that no link exists between ethnic diversity and social trust. The empirical analysis uses individual-level data on social trust from several surveys in Denmark...

Genetic diversity of Streptococcus suis isolates as determined by comparative genome hybridization

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Thi Hoa

2011-07-01

Full Text Available Abstract Background Streptococcus suis is a zoonotic pathogen that causes infections in young piglets. S. suis is a heterogeneous species. Thirty-three different capsular serotypes have been described, that differ in virulence between as well as within serotypes. Results In this study, the correlation between gene content, serotype, phenotype and virulence among 55 S. suis strains was studied using Comparative Genome Hybridization (CGH. Clustering of CGH data divided S. suis isolates into two clusters, A and B. Cluster A isolates could be discriminated from cluster B isolates based on the protein expression of extracellular factor (EF. Cluster A contained serotype 1 and 2 isolates that were correlated with virulence. Cluster B mainly contained serotype 7 and 9 isolates. Genetic similarity was observed between serotype 7 and serotype 2 isolates that do not express muramidase released protein (MRP and EF (MRP-EF-, suggesting these isolates originated from a common founder. Profiles of 25 putative virulence-associated genes of S. suis were determined among the 55 isolates. Presence of all 25 genes was shown for cluster A isolates, whereas cluster B isolates lacked one or more putative virulence genes. Divergence of S. suis isolates was further studied based on the presence of 39 regions of difference. Conservation of genes was evaluated by the definition of a core genome that contained 78% of all ORFs in P1/7. Conclusions In conclusion, we show that CGH is a valuable method to study distribution of genes or gene clusters among isolates in detail, yielding information on genetic similarity, and virulence traits of S. suis isolates.

Life history, population viability, and the potential for local adaptation in isolated trout populations

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K.J. Carim

2017-04-01

Full Text Available Habitat loss and fragmentation have caused population decline across taxa through impacts on life history diversity, dispersal patterns, and gene flow. Yet, intentional isolation of native fish populations is a frequently used management strategy to protect against negative interactions with invasive fish species. We evaluated the population viability and genetic diversity of 12 isolated populations of Oncorhynchus clarkii lewisi located on the Flathead Indian Reservation in Montana, USA. Length-structured integral projection models (IPMs were used to project population growth rate (lambda and its sensitivity to underlying vital rates and parameters. We examined relationships between lambda, genetic diversity, and habitat size and quality. Lambda ranged from 0.68 to 1.1 with 10 of 12 populations projected to be in decline. A sensitivity analysis of lambda with respect to projection matrix elements indicated that lambda was generally sensitive to changes in early life history stages (survival/growth, but patterns differed among populations. Another sensitivity analysis with respect to underlying model parameters showed highly consistent pattern across populations, with lambda being most sensitive to the slope of probability of maturity (estimated from published literature, generally followed by adult survival, and the slope of somatic growth rate (directly measured from each population. Lambda was not correlated with genetic diversity. For populations residing in small isolated streams (≤5 km of occupied habitat, lambda significantly increased with base flow discharge (r2=0.50, p<0.02. Our results highlight the potential importance of local adaptation for persistence of small, isolated populations. Specifically we saw evidence for higher probability of maturity at smaller sizes in the smallest, coldest isolated systems, increasing probability of persistence for these populations. Climate change threatens to further fragment populations of

The Use of Social Media to Combat Research-Isolation.

Science.gov (United States)

Reeve, M A; Partridge, M

2017-09-01

Research-isolation is a common problem affecting many researchers who are disconnected from their research communities. It can be caused by a number of factors, including physical isolation, unfamiliar research topics, diversity, and the nature of the supervisory relationship. All of these aspects can have an impact on both work and the mental health of researchers. Increasingly, researchers are turning to social media for support, by both looking for communities and for increasing the impact of their work. In this paper, we set out a brief introduction to a range of social media platforms used by researchers and present a discussion of the networks within those platforms aimed at reducing research-isolation. These examples highlight just a few of the number of small communities that have grown online to meet the needs of those seeking support through social media. We conclude with some recommendations for those affected by research-isolation and highlight the need for more research into the role of social media on mental health in academics.

Orthogonal typing methods identify genetic diversity among Belgian Campylobacter jejuni strains isolated over a decade from poultry and cases of sporadic human illness.

Science.gov (United States)

Elhadidy, Mohamed; Arguello, Hector; Álvarez-Ordóñez, Avelino; Miller, William G; Duarte, Alexandra; Martiny, Delphine; Hallin, Marie; Vandenberg, Olivier; Dierick, Katelijne; Botteldoorn, Nadine

2018-06-20

Campylobacter jejuni is a zoonotic pathogen commonly associated with human gastroenteritis. Retail poultry meat is a major food-related transmission source of C. jejuni to humans. The present study investigated the genetic diversity, clonal relationship, and strain risk-analysis of 403 representative C. jejuni isolates from chicken broilers (n = 204) and sporadic cases of human diarrhea (n = 199) over a decade (2006-2015) in Belgium, using multilocus sequence typing (MLST), PCR binary typing (P-BIT), and identification of lipooligosaccharide (LOS) biosynthesis locus classes. A total of 123 distinct sequence types (STs), clustered in 28 clonal complexes (CCs) were assigned, including ten novel sequence types that were not previously documented in the international database. Sequence types ST-48, ST-21, ST-50, ST-45, ST-464, ST-2274, ST-572, ST-19, ST-257 and ST-42 were the most prevalent. Clonal complex 21 was the main clonal complex in isolates from humans and chickens. Among observed STs, a total of 35 STs that represent 72.2% (291/403) of the isolates were identified in both chicken and human isolates confirming considerable epidemiological relatedness; these 35 STs also clustered together in the most prevalent CCs. A majority of the isolates harbored sialylated LOS loci associated with potential neuropathic outcomes in humans. Although the concordance between MLST and P-BIT, determined by the adjusted Rand and Wallace coefficients, showed low congruence between both typing methods. The discriminatory power of P-BIT and MLST was similar, with Simpson's diversity indexes of 0.978 and 0.975, respectively. Furthermore, P-BIT could provide additional epidemiological information that would provide further insights regarding the potential association to human health from each strain. In addition, certain clones could be linked to specific clinical symptoms. Indeed, LOS class E was associated with less severe infections. Moreover, ST-572 was significantly

Increase in resistance to extended-spectrum cephalosporins in Salmonella isolated from retail chicken products in Japan.

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Noda, Tamie; Murakami, Koichi; Etoh, Yoshiki; Okamoto, Fuyuki; Yatsuyanagi, Jun; Sera, Nobuyuki; Furuta, Munenori; Onozuka, Daisuke; Oda, Takahiro; Asai, Tetsuo; Fujimoto, Shuji

2015-01-01

Extended-spectrum β-lactamase (ESBL)-producing Salmonella are one of the most important public health problems in developed countries. ESBL-producing Salmonella strains have been isolated from humans in Asian countries neighboring Japan, along with strains harboring the plasmid-mediated extended-spectrum cephalosporin (ESC)-resistance gene, ampC (pAmpC). However, only a few studies have investigated the prevalence of ESC-resistant Salmonella in chicken products in Japan, which are the main vehicle of Salmonella transmission. The aim of this study was to investigate the prevalence of ESBL-producing, pAmpC-harboring, or carbapenem-resistant Salmonella in chicken products in Japan. In total, 355 out of 779 (45.6%) chicken product samples collected from 1996-2010 contained Salmonella, resulting in 378 distinct isolates. Of these isolates, 373 were tested for resistance to ESCs, cephamycins, or carbapenems. Isolates that showed resistance to one or more of these antimicrobials were then examined by PCR and DNA sequence analysis for the presence of the bla(CMY), bla(CTX-M), bla(TEM), and bla(SHV) resistance genes. Thirty-five resistant isolates were detected, including 26 isolates that contained pAmpC (bla(CMY-2)), and nine ESBL-producing isolates harboring bla(CTX-M) (n = 4, consisting of two bla(CTX-M-2) and two bla(CTX-M-15 genes)), bla(TEM) (n = 4, consisting of one bla(TEM-20) and three bla(TEM-52) genes), and bla(SHV) (n = 1, bla(SHV-12)). All pAmpC-harboring and ESBL-producing Salmonella isolates were obtained from samples collected after 2005, and the percentage of resistant isolates increased significantly from 0% in 2004 to 27.9% in 2010 (P for trend = 0.006). This increase was caused in part by an increase in the number of Salmonella enterica subsp. enterica serovar Infantis strains harboring an approximately 280-kb plasmid containing bla(CMY-2) in proximity to ISEcp1. The dissemination of ESC-resistant Salmonella containing plasmid-mediated bla(CMY-2) in

Increase in resistance to extended-spectrum cephalosporins in Salmonella isolated from retail chicken products in Japan.

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Tamie Noda

Full Text Available Extended-spectrum β-lactamase (ESBL-producing Salmonella are one of the most important public health problems in developed countries. ESBL-producing Salmonella strains have been isolated from humans in Asian countries neighboring Japan, along with strains harboring the plasmid-mediated extended-spectrum cephalosporin (ESC-resistance gene, ampC (pAmpC. However, only a few studies have investigated the prevalence of ESC-resistant Salmonella in chicken products in Japan, which are the main vehicle of Salmonella transmission. The aim of this study was to investigate the prevalence of ESBL-producing, pAmpC-harboring, or carbapenem-resistant Salmonella in chicken products in Japan. In total, 355 out of 779 (45.6% chicken product samples collected from 1996-2010 contained Salmonella, resulting in 378 distinct isolates. Of these isolates, 373 were tested for resistance to ESCs, cephamycins, or carbapenems. Isolates that showed resistance to one or more of these antimicrobials were then examined by PCR and DNA sequence analysis for the presence of the bla(CMY, bla(CTX-M, bla(TEM, and bla(SHV resistance genes. Thirty-five resistant isolates were detected, including 26 isolates that contained pAmpC (bla(CMY-2, and nine ESBL-producing isolates harboring bla(CTX-M (n = 4, consisting of two bla(CTX-M-2 and two bla(CTX-M-15 genes, bla(TEM (n = 4, consisting of one bla(TEM-20 and three bla(TEM-52 genes, and bla(SHV (n = 1, bla(SHV-12. All pAmpC-harboring and ESBL-producing Salmonella isolates were obtained from samples collected after 2005, and the percentage of resistant isolates increased significantly from 0% in 2004 to 27.9% in 2010 (P for trend = 0.006. This increase was caused in part by an increase in the number of Salmonella enterica subsp. enterica serovar Infantis strains harboring an approximately 280-kb plasmid containing bla(CMY-2 in proximity to ISEcp1. The dissemination of ESC-resistant Salmonella containing plasmid-mediated bla(CMY-2 in chicken

Prevalence and genetic diversity of Trichomonas vaginalis clinical isolates in a targeted population in Xinxiang City, Henan Province, China.

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Zhang, Zhenchao; Kang, Lixia; Wang, Weijuan; Zhao, Xin; Li, Yuhua; Xie, Qing; Wang, Shuai; He, Tong; Li, Han; Xiao, Tingwei; Chen, Yunchao; Zuo, Suqiong; Kong, Lingmin; Li, Pengju; Li, Xiangrui

2018-03-02

Trichomonas vaginalis (TV) is a protozoan parasite that causes trichomoniasis, a sexually transmitted disease, worldwide. In this study, we investigated the prevalence and genetic characterization of T. vaginalis and contrasted the most prevalent strains of T. vaginalis isolated from Xinxiang City, Henan Province, China. In Xinxiang from September 2015 to September 2017, a total of 267 (1.64%, 95% confidence interval, CI: 1.45-1.85) clinical T. vaginalis-positive samples from vaginal secretions were observed by wet mount microscopy from 16,294 women with some clinical symptoms of trichomoniasis. We found that trichomoniasis frequently occurred in the 21- to 40-year-old age group and in winter. After the 267 clinical T. vaginalis positive samples were cultured, 68 isolates of T. vaginalis were harvested and identified as genotype E (58.82%), H (17.65%), mixed 1 (17.65%) and mixed 2 (5.88%) using a sensitive and reliable polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) typing method on the actin gene. The phylogenetic diversity analysis showed that the genotype E samples fell within a separate clade compared to the other T. vaginalis isolates, while the samples of the genotype H separated into two clades. Our results demonstrate a notable gene polymorphism of clinical isolates from the targeted population and provide insight into the performance of these genetic markers in the molecular epidemiology of trichomoniasis. However, further studies are needed to clarify the association between a certain genotype and the pathogenicity of T. vaginalis.

Sequence diversities of serine-aspartate repeat genes among Staphylococcus aureus isolates from different hosts presumably by horizontal gene transfer.

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Huping Xue

Full Text Available BACKGROUND: Horizontal gene transfer (HGT is recognized as one of the major forces for bacterial genome evolution. Many clinically important bacteria may acquire virulence factors and antibiotic resistance through HGT. The comparative genomic analysis has become an important tool for identifying HGT in emerging pathogens. In this study, the Serine-Aspartate Repeat (Sdr family has been compared among different sources of Staphylococcus aureus (S. aureus to discover sequence diversities within their genomes. METHODOLOGY/PRINCIPAL FINDINGS: Four sdr genes were analyzed for 21 different S. aureus strains and 218 mastitis-associated S. aureus isolates from Canada. Comparative genomic analyses revealed that S. aureus strains from bovine mastitis (RF122 and mastitis isolates in this study, ovine mastitis (ED133, pig (ST398, chicken (ED98, and human methicillin-resistant S. aureus (MRSA (TCH130, MRSA252, Mu3, Mu50, N315, 04-02981, JH1 and JH9 were highly associated with one another, presumably due to HGT. In addition, several types of insertion and deletion were found in sdr genes of many isolates. A new insertion sequence was found in mastitis isolates, which was presumably responsible for the HGT of sdrC gene among different strains. Moreover, the sdr genes could be used to type S. aureus. Regional difference of sdr genes distribution was also indicated among the tested S. aureus isolates. Finally, certain associations were found between sdr genes and subclinical or clinical mastitis isolates. CONCLUSIONS: Certain sdr gene sequences were shared in S. aureus strains and isolates from different species presumably due to HGT. Our results also suggest that the distributional assay of virulence factors should detect the full sequences or full functional regions of these factors. The traditional assay using short conserved regions may not be accurate or credible. These findings have important implications with regard to animal husbandry practices that may

Diversity of endophytic fungal and bacterial communities in Ilex paraguariensis grown under field conditions.

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Pérez, María Laura; Collavino, Mónica Mariana; Sansberro, Pedro Alfonso; Mroginski, Luis Amado; Galdeano, Ernestina

2016-04-01

The composition and diversity of the endophytic community associated with yerba mate (Ilex paraguariensis) was investigated using culture-depending methods. Fungi were identified based on their micromorphological characteristics and internal transcribed spacer rDNA sequence analysis; for bacteria 16S rDNA sequence analysis was used. Fungal and bacterial diversity did not show significant differences between organ age. The highest fungal diversity was registered during fall season and the lowest in winter. Bacterial diversity was higher in stems and increased from summer to winter, in contrast with leaves, which decreased. The most frequently isolated fungus was Fusarium, followed by Colletotrichum; they were both present in all the sampling seasons and organ types assayed. Actinobacteria represented 57.5 % of all bacterial isolates. The most dominant bacterial taxa were Curtobacterium and Microbacterium. Other bacteria frequently found were Methylobacterium, Sphingomonas, Herbiconiux and Bacillus. Nitrogen fixation and phosphate solubilization activity, ACC deaminase production and antagonism against plant fungal pathogens were assayed in endophytic bacterial strains. In the case of fungi, strains of Trichoderma, Penicillium and Aspergillus were assayed for antagonism against pathogenic Fusarium sp. All microbial isolates assayed showed at least one growth promoting activity. Strains of Bacillus, Pantoea, Curtobacterium, Methylobacterium, Brevundimonas and Paenibacillus had at least two growth-promoting activities, and Bacillus, Paenibacillus and the three endophytic fungi showed high antagonistic activity against Fusarium sp. In this work we have made a wide study of the culturable endophytic community within yerba mate plants and found that several microbial isolates could be considered as potential inoculants useful for improving yerba mate production.

Genetic Characterization of a Panel of Diverse HIV-1 Isolates at Seven International Sites.

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Bhavna Hora

Full Text Available HIV-1 subtypes and drug resistance are routinely tested by many international surveillance groups. However, results from different sites often vary. A systematic comparison of results from multiple sites is needed to determine whether a standardized protocol is required for consistent and accurate data analysis. A panel of well-characterized HIV-1 isolates (N = 50 from the External Quality Assurance Program Oversight Laboratory (EQAPOL was assembled for evaluation at seven international sites. This virus panel included seven subtypes, six circulating recombinant forms (CRFs, nine unique recombinant forms (URFs and three group O viruses. Seven viruses contained 10 major drug resistance mutations (DRMs. HIV-1 isolates were prepared at a concentration of 107 copies/ml and compiled into blinded panels. Subtypes and DRMs were determined with partial or full pol gene sequences by conventional Sanger sequencing and/or Next Generation Sequencing (NGS. Subtype and DRM results were reported and decoded for comparison with full-length genome sequences generated by EQAPOL. The partial pol gene was amplified by RT-PCR and sequenced for 89.4%-100% of group M viruses at six sites. Subtyping results of majority of the viruses (83%-97.9% were correctly determined for the partial pol sequences. All 10 major DRMs in seven isolates were detected at these six sites. The complete pol gene sequence was also obtained by NGS at one site. However, this method missed six group M viruses and sequences contained host chromosome fragments. Three group O viruses were only characterized with additional group O-specific RT-PCR primers employed by one site. These results indicate that PCR protocols and subtyping tools should be standardized to efficiently amplify diverse viruses and more consistently assign virus genotypes, which is critical for accurate global subtype and drug resistance surveillance. Targeted NGS analysis of partial pol sequences can serve as an alternative

Genotypic diversity of multidrug-, quinolone- and extensively drug-resistant Mycobacterium tuberculosis isolates in Thailand.

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Disratthakit, Areeya; Meada, Shinji; Prammananan, Therdsak; Thaipisuttikul, Iyarit; Doi, Norio; Chaiprasert, Angkana

2015-06-01

Drug-resistant tuberculosis (TB), which includes multidrug-resistant (MDR-TB), quinolone-resistant (QR-TB) and extensively drug-resistant tuberculosis (XDR-TB), is a serious threat to TB control. We aimed to characterize the genotypic diversity of drug-resistant TB clinical isolates collected in Thailand to establish whether the emergence of drug-resistant TB is attributable to transmitted resistance or acquired resistance. We constructed the first molecular phylogeny of MDR-TB (n=95), QR-TB (n=69) and XDR-TB (n=28) in Thailand based on spoligotyping and proposed 24-locus multilocus variable-number of tandem repeat analysis (MLVA). Clustering analysis was performed using the unweighted pair group method with arithmetic mean. Spoligotyping identified the Beijing strain (SIT1) as the most predominant genotype (n=139; 72.4%). The discriminatory power of 0.9235 Hunter-Gaston Discriminatory Index (HGDI) with the 15-locus variable-number tandem repeats of mycobacterial interspersed repetitive units typing was improved to a 0.9574 HGDI with proposed 24-locus MLVA, thereby resulting in the subdivision of a large cluster of Beijing strains (SIT1) into 17 subclusters. We identified the spread of drug-resistant TB clones caused by three different MLVA types in the Beijing strain (SIT1) and a specific clone of XDR-TB caused by a rare genotype, the Manu-ancestor strain (SIT523). Overall, 49.5% of all isolates were clustered. These findings suggest that a remarkable transmission of drug-resistant TB occurred in Thailand. The remaining 50% of drug-resistant TB isolates were unique genotypes, which may have arisen from the individual acquisition of drug resistance. Our results suggest that transmitted and acquired resistance have played an equal role in the emergence of drug-resistant TB. Further characterization of whole genome sequences of clonal strains could help to elucidate the mycobacterial genetic factors relevant for drug resistance, transmissibility and virulence

Genotypic Diversity of Phytophthora cinnamomi and P. plurivora in Maryland's Nurseries and Mid-Atlantic Forests.

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Beaulieu, Justine; Ford, Blaine; Balci, Yilmaz

2017-06-01

Genetic diversity of two Phytophthora spp.-P. cinnamomi (102 isolates), commonly encountered in Maryland nurseries and forests in the Mid-Atlantic United States, and P. plurivora (186 isolates), a species common in nurseries-was characterized using amplified fragment length polymorphism. Expected heterozygosity and other indices suggested a lower level of diversity among P. cinnamomi than P. plurivora isolates. Hierarchical clustering showed P. cinnamomi isolates separated into four clusters, and two of the largest clusters were closely related, containing 80% of the isolates. In contrast, P. plurivora isolates separated into six clusters, one of which included approximately 40% of the isolates. P. plurivora isolates recovered from the environment (e.g., soil and water) were genotypically more diverse than those found causing lesions. For both species, isolate origin (forest versus nursery or among nurseries) was a significant factor of heterozygosity. Clonal groups existed within P. cinnamomi and P. plurivora and included isolates from both forest and nurseries, suggesting that a pathway from nurseries to forests or vice versa exists.

Diverse Burkholderia Species Isolated from Soils in the Southern United States with No Evidence of B. pseudomallei.

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Carina M Hall

Full Text Available The global distribution of the soil-dwelling bacterium Burkholderia pseudomallei, causative agent of melioidosis, is poorly understood. We used established culturing methods developed for B. pseudomallei to isolate Burkholderia species from soil collected at 18 sampling sites in three states in the southern United States (Arizona (n = 4, Florida (n = 7, and Louisiana (n = 7. Using multi-locus sequence typing (MLST of seven genes, we identified 35 Burkholderia isolates from these soil samples. All species belonged to the B. cepacia complex (Bcc, including B. cenocepacia, B. cepacia, B. contaminans, B. diffusa, B. metallica, B. seminalis, B. vietnamiensis and two unnamed members of the Bcc. The MLST analysis provided a high level of resolution among and within these species. Despite previous clinical cases within the U.S. involving B. pseudomallei and its close phylogenetic relatives, we did not isolate any of these taxa. The Bcc contains a number of opportunistic pathogens that cause infections in cystic fibrosis patients. Interestingly, we found that B. vietnamiensis was present in soil from all three states, suggesting it may be a common component in southern U.S. soils. Most of the Burkholderia isolates collected in this study were from Florida (30/35; 86%, which may be due to the combination of relatively moist, sandy, and acidic soils found there compared to the other two states. We also investigated one MLST gene, recA, for its ability to identify species within Burkholderia. A 365bp fragment of recA recovered nearly the same species-level identification as MLST, thus demonstrating its cost effective utility when conducting environmental surveys for Burkholderia. Although we did not find B. pseudomallei, our findings document that other diverse Burkholderia species are present in soils in the southern United States.

Diverse Burkholderia Species Isolated from Soils in the Southern United States with No Evidence of B. pseudomallei.

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Hall, Carina M; Busch, Joseph D; Shippy, Kenzie; Allender, Christopher J; Kaestli, Mirjam; Mayo, Mark; Sahl, Jason W; Schupp, James M; Colman, Rebecca E; Keim, Paul; Currie, Bart J; Wagner, David M

2015-01-01

The global distribution of the soil-dwelling bacterium Burkholderia pseudomallei, causative agent of melioidosis, is poorly understood. We used established culturing methods developed for B. pseudomallei to isolate Burkholderia species from soil collected at 18 sampling sites in three states in the southern United States (Arizona (n = 4), Florida (n = 7), and Louisiana (n = 7)). Using multi-locus sequence typing (MLST) of seven genes, we identified 35 Burkholderia isolates from these soil samples. All species belonged to the B. cepacia complex (Bcc), including B. cenocepacia, B. cepacia, B. contaminans, B. diffusa, B. metallica, B. seminalis, B. vietnamiensis and two unnamed members of the Bcc. The MLST analysis provided a high level of resolution among and within these species. Despite previous clinical cases within the U.S. involving B. pseudomallei and its close phylogenetic relatives, we did not isolate any of these taxa. The Bcc contains a number of opportunistic pathogens that cause infections in cystic fibrosis patients. Interestingly, we found that B. vietnamiensis was present in soil from all three states, suggesting it may be a common component in southern U.S. soils. Most of the Burkholderia isolates collected in this study were from Florida (30/35; 86%), which may be due to the combination of relatively moist, sandy, and acidic soils found there compared to the other two states. We also investigated one MLST gene, recA, for its ability to identify species within Burkholderia. A 365bp fragment of recA recovered nearly the same species-level identification as MLST, thus demonstrating its cost effective utility when conducting environmental surveys for Burkholderia. Although we did not find B. pseudomallei, our findings document that other diverse Burkholderia species are present in soils in the southern United States.

Diversity of Moraxella spp. strains recovered from infectious bovine keratoconjunctivitis cases in Uruguay.

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Sosa, Vanessa; Zunino, Pablo

2013-11-15

Infectious bovine keratoconjunctivitis (IBK) is the most common ocular disease that affects cattle throughout the world and it has a very significant economic impact. IBK is caused by members of the genus Moraxella and therapeutic and preventive measures have shown limited success. Vaccines, most of them chemically inactivated bacterins, generally induce a limited protection. In this study, the genetic diversity of Uruguayan clinical Moraxella bovis and Moraxella bovoculi isolates was assessed by RAPD-PCR, ERIC-PCR and BOX-PCR fingerprinting. Also, antibiotic resistance of the Moraxella spp. isolates was assessed utilizing the disk diffusion method. When interspecific molecular diversity was assessed, different bands patterns were observed even within a single outbreak of IBK, showing the coexistence of different genotypes of Moraxella spp. The high genetic diversity within M. bovis and M. bovoculi isolates did not permit to correlate isolates DNA fingerprints with geographical origins, dates or even with both different Moraxella species. Antibiotics resistance patterns showed significant differences between M. bovis and M. bovoculi. This is the first study of diversity that includes M. bovis and M. bovoculi associated to IBK cases. Genetic diversity did not allow to correlate DNA fingerprints of the isolates with geographical origins, isolation dates or even both different Moraxella species. Antibiotics resistance patterns showed differences between M. bovis and M. bovoculi. This remarkable variation within isolates could explain the partial protection induced by commercial vaccines. All these findings could be important for the design of prevention or treatment strategies against IBK.

Diversity and enzymatic characterization of Bacillus species isolated ...

African Journals Online (AJOL)

Fermentation plays an important role in the production of cassava-based foods in West Africa. In Côte ... microorganisms (lactic acid bacteria, yeast and moulds ..... Bacillus species isolated from solid substrate fermentation of cassava for.

Diversity of phytases in the rumen.

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Nakashima, Brenda A; McAllister, Tim A; Sharma, Ranjana; Selinger, L Brent

2007-01-01

Examples of a new class of phytase related to protein tyrosine phosphatases (PTP) were recently isolated from several anaerobic bacteria from the rumen of cattle. In this study, the diversity of PTP-like phytase gene sequences in the rumen was surveyed by using the polymerase chain reaction (PCR). Two sets of degenerate primers were used to amplify sequences from rumen fluid total community DNA and genomic DNA from nine bacterial isolates. Four novel PTP-like phytase sequences were retrieved from rumen fluid, whereas all nine of the anaerobic bacterial isolates investigated in this work contained PTP-like phytase sequences. One isolate, Selenomonas lacticifex, contained two distinct PTP-like phytase sequences, suggesting that multiple phytate hydrolyzing enzymes are present in this bacterium. The degenerate primer and PCR conditions described here, as well as novel sequences obtained in this study, will provide a valuable resource for future studies on this new class of phytase. The observed diversity of microbial phytases in the rumen may account for the ability of ruminants to derive a significant proportion of their phosphorus requirements from phytate.

Forest-to-pasture conversion increases the diversity of the phylum Verrucomicrobia in Amazon rainforest soils.

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Ranjan, Kshitij; Paula, Fabiana S; Mueller, Rebecca C; Jesus, Ederson da C; Cenciani, Karina; Bohannan, Brendan J M; Nüsslein, Klaus; Rodrigues, Jorge L M

2015-01-01

The Amazon rainforest is well known for its rich plant and animal diversity, but its bacterial diversity is virtually unexplored. Due to ongoing and widespread deforestation followed by conversion to agriculture, there is an urgent need to quantify the soil biological diversity within this tropical ecosystem. Given the abundance of the phylum Verrucomicrobia in soils, we targeted this group to examine its response to forest-to-pasture conversion. Both taxonomic and phylogenetic diversities were higher for pasture in comparison to primary and secondary forests. The community composition of Verrucomicrobia in pasture soils was significantly different from those of forests, with a 11.6% increase in the number of sequences belonging to subphylum 3 and a proportional decrease in sequences belonging to the class Spartobacteria. Based on 99% operational taxonomic unit identity, 40% of the sequences have not been detected in previous studies, underscoring the limited knowledge regarding the diversity of microorganisms in tropical ecosystems. The abundance of Verrucomicrobia, measured with quantitative PCR, was strongly correlated with soil C content (r = 0.80, P = 0.0016), indicating their importance in metabolizing plant-derived carbon compounds in soils.

Vector species richness increases haemorrhagic disease prevalence through functional diversity modulating the duration of seasonal transmission.

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Park, Andrew W; Cleveland, Christopher A; Dallas, Tad A; Corn, Joseph L

2016-06-01

Although many parasites are transmitted between hosts by a suite of arthropod vectors, the impact of vector biodiversity on parasite transmission is poorly understood. Positive relationships between host infection prevalence and vector species richness (SR) may operate through multiple mechanisms, including (i) increased vector abundance, (ii) a sampling effect in which species of high vectorial capacity are more likely to occur in species-rich communities, and (iii) functional diversity whereby communities comprised species with distinct phenologies may extend the duration of seasonal transmission. Teasing such mechanisms apart is impeded by a lack of appropriate data, yet could highlight a neglected role for functional diversity in parasite transmission. We used statistical modelling of extensive host, vector and microparasite data to test the hypothesis that functional diversity leading to longer seasonal transmission explained variable levels of disease in a wildlife population. We additionally developed a simple transmission model to guide our expectation of how an increased transmission season translates to infection prevalence. Our study demonstrates that vector SR is associated with increased levels of disease reporting, but not via increases in vector abundance or via a sampling effect. Rather, the relationship operates by extending the length of seasonal transmission, in line with theoretical predictions.

Plasmodium vivax merozoite surface protein-3 alpha: a high-resolution marker for genetic diversity studies.

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Prajapati, Surendra Kumar; Joshi, Hema; Valecha, Neena

2010-06-01

Malaria, an ancient human infectious disease caused by five species of Plasmodium, among them Plasmodium vivax is the most widespread human malaria species and causes huge morbidity to its host. Identification of genetic marker to resolve higher genetic diversity for an ancient origin organism is a crucial task. We have analyzed genetic diversity of P. vivax field isolates using highly polymorphic antigen gene merozoite surface protein-3 alpha (msp-3 alpha) and assessed its suitability as high-resolution genetic marker for population genetic studies. 27 P. vivax field isolates collected during chloroquine therapeutic efficacy study at Chennai were analyzed for genetic diversity. PCR-RFLP was employed to assess the genetic variations using highly polymorphic antigen gene msp-3 alpha. We observed three distinct PCR alleles at msp-3 alpha, and among them allele A showed significantly high frequency (53%, chi2 = 8.22, p = 0.001). PCR-RFLP analysis revealed 14 and 17 distinct RFLP patterns for Hha1 and Alu1 enzymes respectively. Further, RFLP analysis revealed that allele A at msp-3 alpha is more diverse in the population compared with allele B and C. Combining Hha1 and Alu1 RFLP patterns revealed 21 distinct genotypes among 22 isolates reflects higher diversity resolution power of msp-3 alpha in the field isolates. P. vivax isolates from Chennai region revealed substantial amount of genetic diversity and comparison of allelic diversity with other antigen genes and microsatellites suggesting that msp-3 alpha could be a high-resolution marker for genetic diversity studies among P. vivax field isolates.

High and distinct range-edge genetic diversity despite local bottlenecks.

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Jorge Assis

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

Characterisation of the genetic diversity of Brucella by multilocus sequencing

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MacMillan Alastair P

2007-04-01

Full Text Available Abstract Background Brucella species include economically important zoonotic pathogens that can infect a wide range of animals. There are currently six classically recognised species of Brucella although, as yet unnamed, isolates from various marine mammal species have been reported. In order to investigate genetic relationships within the group and identify potential diagnostic markers we have sequenced multiple genetic loci from a large sample of Brucella isolates representing the known diversity of the genus. Results Nine discrete genomic loci corresponding to 4,396 bp of sequence were examined from 160 Brucella isolates. By assigning each distinct allele at a locus an arbitrary numerical designation the population was found to represent 27 distinct sequence types (STs. Diversity at each locus ranged from 1.03–2.45% while overall genetic diversity equated to 1.5%. Most loci examined represent housekeeping gene loci and, in all but one case, the ratio of non-synonymous to synonymous change was substantially Brucella species, B. abortus, B. melitensis, B. ovis and B. neotomae correspond to well-separated clusters. With the exception of biovar 5, B. suis isolates cluster together, although they form a more diverse group than other classical species with a number of distinct STs corresponding to the remaining four biovars. B. canis isolates are located on the same branch very closely related to, but distinguishable from, B. suis biovar 3 and 4 isolates. Marine mammal isolates represent a distinct, though rather weakly supported, cluster within which individual STs display one of three clear host preferences. Conclusion The sequence database provides a powerful dataset for addressing ongoing controversies in Brucella taxonomy and a tool for unambiguously placing atypical, phenotypically discordant or newly emerging Brucella isolates. Furthermore, by using the phylogenetic backbone described here, robust and rationally selected markers for use in

Diverse deep-sea fungi from the South China Sea and their antimicrobial activity.

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Zhang, Xiao-Yong; Zhang, Yun; Xu, Xin-Ya; Qi, Shu-Hua

2013-11-01

We investigated the diversity of fungal communities in nine different deep-sea sediment samples of the South China Sea by culture-dependent methods followed by analysis of fungal internal transcribed spacer (ITS) sequences. Although 14 out of 27 identified species were reported in a previous study, 13 species were isolated from sediments of deep-sea environments for the first report. Moreover, these ITS sequences of six isolates shared 84-92 % similarity with their closest matches in GenBank, which suggested that they might be novel phylotypes of genera Ajellomyces, Podosordaria, Torula, and Xylaria. The antimicrobial activities of these fungal isolates were explored using a double-layer technique. A relatively high proportion (56 %) of fungal isolates exhibited antimicrobial activity against at least one pathogenic bacterium or fungus among four marine pathogenic microbes (Micrococcus luteus, Pseudoaltermonas piscida, Aspergerillus versicolor, and A. sydowii). Out of these antimicrobial fungi, the genera Arthrinium, Aspergillus, and Penicillium exhibited antibacterial and antifungal activities, while genus Aureobasidium displayed only antibacterial activity, and genera Acremonium, Cladosporium, Geomyces, and Phaeosphaeriopsis displayed only antifungal activity. To our knowledge, this is the first report to investigate the diversity and antimicrobial activity of culturable deep-sea-derived fungi in the South China Sea. These results suggest that diverse deep-sea fungi from the South China Sea are a potential source for antibiotics' discovery and further increase the pool of fungi available for natural bioactive product screening.

In vitro anticancer activity of microbial isolates from diverse habitats

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Angel Treasa Thomas

2011-06-01

Full Text Available Extracts from natural products, especially microorganisms, have served as a valuable source of diverse molecules in many drug discovery efforts and led to the discovery of several important drugs. Identification of microbial strains having promising biological activities and purifying the bio-molecules responsible for the activities, have led to the discovery of many bioactive molecules. Extracellular, as well as intracellular, extracts of the metabolites of thirty-six bacterial and twenty-four fungal isolates, grown under unusual conditions such as high temperature, high salt and low sugar concentrations, were in vitro tested for their cytotoxic potential on various cancer cell lines. The extracts were screened on HeLa and MCF-7 cell lines to study the cytotoxic potential. Nuclear staining and flow cytometric studies were carried out to assess the potential of the extracts in arresting the cell cycle. The crude ethylacetate extract of isolate F-21 showed promising results by MTT assay with IC50 as low as 20.37±0.36 µg/mL on HeLa, and 44.75±0.81 µg/mL on MCF-7 cells, comparable with Cisplatin. The isolate F-21 was identified as Aspergillus sp. Promising results were also obtained with B-2C and B-4E strains. Morphological studies, biochemical tests and preliminary chemical investigation of the extracts were also carried out.Extratos de produtos naturais, especialmente de microrganismos, constituíram-se em fonte valiosa de diversas moléculas em muitas descobertas de fármacos e levaram à descoberta de fármacos importantes. A identificação de espécies microbianas que apresentam atividade biológica e a purificação de biomoléculas responsáveis pelas atividades levou à descoberta de muitas moléculas bioativas. Extratos extracelulares tanto quanto intracelulares de metabólitos de 36 isolados de bactérias e 24 isolados de fungos, que cresceram sob condições não usuais, como alta temperatura, alta concentração de sal e baixa

The uses of AFLP for detecting DNA polymorphism, genotype identification and genetic diversity between yeasts isolated from Mexican agave-distilled beverages and from grape musts.

Science.gov (United States)

Flores Berrios, E P; Alba González, J F; Arrizon Gaviño, J P; Romano, P; Capece, A; Gschaedler Mathis, A

2005-01-01

The objectives were to determine the variability and to compare the genetic diversity obtained using amplified fragment length polymorphism (AFLP) markers in analyses of wine, tequila, mezcal, sotol and raicilla yeasts. A molecular characterization of yeasts isolated from Mexican agave musts, has been performed by AFLP marker analysis, using reference wine strains from Italian and South African regions. A direct co-relation between genetic profile, origin and fermentation process of strains was found especially in strains isolated from agave must. In addition, unique molecular markers were obtained for all the strains using six combination primers, confirming the discriminatory power of AFLP markers. This is the first report of molecular characterization between yeasts isolated from different Mexican traditional agave-distilled beverages, which shows high genetic differences with respect to wine strains.

Genetic diversity of Mycobacterium tuberculosis in Mbarara, South ...

African Journals Online (AJOL)

Background: We determined the genetic diversity of mycobacteria isolated from tuberculosis patients in Mbarara Uganda, using region of difference (RD) analysis and spacer oligonucleotide typing (spoligotyping). Methods: Sputum samples were cultured on Lowenstein Jensen media. The isolates were characterized using ...

Buried straw layer and plastic mulching increase microlfora diversity in salinized soil

Institute of Scientific and Technical Information of China (English)

LI Yu-yi; PANG Huan-cheng; HAN Xiu-fang; YAN Shou-wei; ZHAO Yong-gan; WANG Jing; ZHAI Zhen; ZHANG Jian-li

2016-01-01

Salt stress has been increasingly constraining crop productivity in arid lands of the world. In our recent study, salt stress was aleviated and crop productivity was improved remarkably by straw layer burial plus plastic iflm mulching in a saline soil. However, its impact on the microlfora diversity is not wel documented. Field micro-plot experiments were conducted from 2010 to 2011 using four tilage methods: (i) deep tilage with plastic iflm mulching (CK), (i) straw layer burial at 40 cm (S), (ii) straw layer burial plus surface soil mulching with straw material (S+S), and (iv) plastic iflm mulching plus buried straw layer (P+S). Culturable microbes and predominant bacterial communities were studied; based on 16S rDNA, bacterial com-munity structure and abundance were characterized using denaturing gradient gel electrophoresis (DGGE) and polymerase chain reaction (PCR). Results showed that P+S was the most favorable for culturable bacteria, actinomyces and fungi and induced the most diverse genera of bacteria compared to other tilage methods. Soil temperature had signiifcant positive correlations with the number of bacteria, actinomyces and fungi (P<0.01). However, soil water was poorly correlated with any of the microbes. Salt content had a signiifcant negative correlation with the number of microbers, especialy for bacteria and fungi (P<0.01). DGGE analysis showed that the P+S exhibited the highest diversity of bacteria with 20 visible bands folowed by S+S, S and CK. Moreover, P+S had the highest similarity (68%) of bacterial communities with CK. The major bacterial genera in al soil samples wereFirmicutes,Proteobacteria andActinobacteria. Given the considerable increase in microbial growth, the combined use of straw layer burial and plastic iflm mulching could be a practical option for aleviating salt stress effects on soil microbial community and thereby improving crop production in arid saline soils.

Rapid Increases in forest understory diversity and productivity following a mountain pine beetle (Dendroctonus ponderosae) outbreak in pine forests.

Science.gov (United States)

Pec, Gregory J; Karst, Justine; Sywenky, Alexandra N; Cigan, Paul W; Erbilgin, Nadir; Simard, Suzanne W; Cahill, James F

2015-01-01

The current unprecedented outbreak of mountain pine beetle (Dendroctonus ponderosae) in lodgepole pine (Pinus contorta) forests of western Canada has resulted in a landscape consisting of a mosaic of forest stands at different stages of mortality. Within forest stands, understory communities are the reservoir of the majority of plant species diversity and influence the composition of future forests in response to disturbance. Although changes to stand composition following beetle outbreaks are well documented, information on immediate responses of forest understory plant communities is limited. The objective of this study was to examine the effects of D. ponderosae-induced tree mortality on initial changes in diversity and productivity of understory plant communities. We established a total of 110 1-m2 plots across eleven mature lodgepole pine forests to measure changes in understory diversity and productivity as a function of tree mortality and below ground resource availability across multiple years. Overall, understory community diversity and productivity increased across the gradient of increased tree mortality. Richness of herbaceous perennials increased with tree mortality as well as soil moisture and nutrient levels. In contrast, the diversity of woody perennials did not change across the gradient of tree mortality. Understory vegetation, namely herbaceous perennials, showed an immediate response to improved growing conditions caused by increases in tree mortality. How this increased pulse in understory richness and productivity affects future forest trajectories in a novel system is unknown.

Rapid Increases in forest understory diversity and productivity following a mountain pine beetle (Dendroctonus ponderosae outbreak in pine forests.

Directory of Open Access Journals (Sweden)

Gregory J Pec

Full Text Available The current unprecedented outbreak of mountain pine beetle (Dendroctonus ponderosae in lodgepole pine (Pinus contorta forests of western Canada has resulted in a landscape consisting of a mosaic of forest stands at different stages of mortality. Within forest stands, understory communities are the reservoir of the majority of plant species diversity and influence the composition of future forests in response to disturbance. Although changes to stand composition following beetle outbreaks are well documented, information on immediate responses of forest understory plant communities is limited. The objective of this study was to examine the effects of D. ponderosae-induced tree mortality on initial changes in diversity and productivity of understory plant communities. We established a total of 110 1-m2 plots across eleven mature lodgepole pine forests to measure changes in understory diversity and productivity as a function of tree mortality and below ground resource availability across multiple years. Overall, understory community diversity and productivity increased across the gradient of increased tree mortality. Richness of herbaceous perennials increased with tree mortality as well as soil moisture and nutrient levels. In contrast, the diversity of woody perennials did not change across the gradient of tree mortality. Understory vegetation, namely herbaceous perennials, showed an immediate response to improved growing conditions caused by increases in tree mortality. How this increased pulse in understory richness and productivity affects future forest trajectories in a novel system is unknown.

Increasing Cropping System Diversity Balances Productivity, Profitability and Environmental Health

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Davis, Adam S.; Hill, Jason D.; Chase, Craig A.; Johanns, Ann M.; Liebman, Matt

2012-01-01

Balancing productivity, profitability, and environmental health is a key challenge for agricultural sustainability. Most crop production systems in the United States are characterized by low species and management diversity, high use of fossil energy and agrichemicals, and large negative impacts on the environment. We hypothesized that cropping system diversification would promote ecosystem services that would supplement, and eventually displace, synthetic external inputs used to maintain crop productivity. To test this, we conducted a field study from 2003–2011 in Iowa that included three contrasting systems varying in length of crop sequence and inputs. We compared a conventionally managed 2-yr rotation (maize-soybean) that received fertilizers and herbicides at rates comparable to those used on nearby farms with two more diverse cropping systems: a 3-yr rotation (maize-soybean-small grain + red clover) and a 4-yr rotation (maize-soybean-small grain + alfalfa-alfalfa) managed with lower synthetic N fertilizer and herbicide inputs and periodic applications of cattle manure. Grain yields, mass of harvested products, and profit in the more diverse systems were similar to, or greater than, those in the conventional system, despite reductions of agrichemical inputs. Weeds were suppressed effectively in all systems, but freshwater toxicity of the more diverse systems was two orders of magnitude lower than in the conventional system. Results of our study indicate that more diverse cropping systems can use small amounts of synthetic agrichemical inputs as powerful tools with which to tune, rather than drive, agroecosystem performance, while meeting or exceeding the performance of less diverse systems. PMID:23071739

The interplay of diversity training and diversity beliefs on team creativity in nationality diverse teams.

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Homan, Astrid C; Buengeler, Claudia; Eckhoff, Robert A; van Ginkel, Wendy P; Voelpel, Sven C

2015-09-01

Attaining value from nationality diversity requires active diversity management, which organizations often employ in the form of diversity training programs. Interestingly, however, the previously reported effects of diversity training are often weak and, sometimes, even negative. This situation calls for research on the conditions under which diversity training helps or harms teams. We propose that diversity training can increase team creativity, but only for teams with less positive pretraining diversity beliefs (i.e., teams with a greater need for such training) and that are sufficiently diverse in nationality. Comparing the creativity of teams that attended nationality diversity training versus control training, we found that for teams with less positive diversity beliefs, diversity training increased creative performance when the team's nationality diversity was high, but undermined creativity when the team's nationality diversity was low. Diversity training had less impact on teams with more positive diversity beliefs, and training effects were not contingent upon these teams' diversity. Speaking to the underlying process, we showed that these interactive effects were driven by the experienced team efficacy of the team members. We discuss theoretical and practical implications for nationality diversity management. (c) 2015 APA, all rights reserved).

Endophytic Fungal Diversity in Medicinal Plants of Western Ghats, India

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Monnanda Somaiah Nalini

2014-01-01

Full Text Available Endophytes constitute an important component of microbial diversity, and in the present investigation, seven plant species with rich ethnobotanical uses representing six families were analyzed for the presence of endophytic fungi from their natural habitats during monsoon (May/June and winter (November/December seasons of 2007. Fungal endophytes were isolated from healthy plant parts such as stem, root, rhizome, and inflorescence employing standard isolation methods. One thousand five hundred and twenty-nine fungal isolates were obtained from 5200 fragments. Stem fragments harbored more endophytes (80.37% than roots (19.22%. 31 fungal taxa comprised of coelomycetes (65%, hyphomycetes (32%, and ascomycetes (3%. Fusarium, Acremonium, Colletotrichum, Chaetomium, Myrothecium, Phomopsis, and Pestalotiopsis spp. were commonly isolated. Diversity indices differed significantly between the seasons (P<0.001. Species richness was greater for monsoon isolations than winter. Host specificity was observed for few fungal endophytes. UPGMA cluster analysis grouped the endophytes into distinct clusters on the basis of genetic distance. This study is the first report on the diversity and host-specificity of endophytic fungal taxa were from the semi evergreen forest type in Talacauvery subcluster of Western Ghats.

Genetic relatedness among Campylobacter jejuni serotyped isolates of diverse origin as determined by numerical analysis of amplified fragment length polymorphism (AFLP) profiles

DEFF Research Database (Denmark)

Siemer, B.L.; Harrington, C.S.; Nielsen, E.M.

2004-01-01

health. The remaining 30 groups contained isolates from humans, chickens and associated food products, cattle, sheep, turkeys, ostriches and/or dogs. Strains assigned to serotypes 2, 6/7, 11 and 12 formed major clusters at the 77.6% S-level. Most other serotypes did not form homogeneous clusters....... conclusions: High-resolution genotyping applied to strains from a comprehensive range of sources provides evidence for multiple sources of sporadic C. jejuni infection. The results suggest that public health protection measures should be directed at all foods of animal origin. Significance and Impct...... diarrhoea and diverse animal and environmental sources were collected mainly through a National surveillance programme in Denmark and serotyped by use of the established 'Penner' scheme. Genetic relationships among these isolates, and the archetypal serotype reference strains, were assessed by numerical...

Now hiring! Empirically testing a three-step intervention to increase faculty gender diversity in STEM

Science.gov (United States)

Smith, Jessi L.; Handley, Ian M.; Zale, Alexander V.; Rushing, Sara; Potvin, Martha A.

2015-01-01

Workforce homogeneity limits creativity, discovery, and job satisfaction; nonetheless, the vast majority of university faculty in science, technology, engineering, and mathematics (STEM) fields are men. We conducted a randomized and controlled three-step faculty search intervention based in self-determination theory aimed at increasing the number of women faculty in STEM at one US university where increasing diversity had historically proved elusive. Results show that the numbers of women candidates considered for and offered tenure-track positions were significantly higher in the intervention groups compared with those in controls. Searches in the intervention were 6.3 times more likely to make an offer to a woman candidate, and women who were made an offer were 5.8 times more likely to accept the offer from an intervention search. Although the focus was on increasing women faculty within STEM, the intervention can be adapted to other scientific and academic communities to advance diversity along any dimension.

Microsatellite analysis of Saccharomyces uvarum diversity.

Science.gov (United States)

Masneuf-Pomarede, Isabelle; Salin, Franck; Börlin, Marine; Coton, Emmanuel; Coton, Monika; Jeune, Christine Le; Legras, Jean-Luc

2016-03-01

Considered as a sister species of Saccharomyces cerevisiae, S. uvarum is, to a lesser extent, an interesting species for fundamental and applied research studies. Despite its potential interest as a new gene pool for fermenting agents, the intraspecific molecular genetic diversity of this species is still poorly investigated. In this study, we report the use of nine microsatellite markers to describe S. uvarum genetic diversity and population structure among 108 isolates from various geographical and substrate origins (wine, cider and natural sources). Our combined microsatellite markers set allowed differentiating 89 genotypes. In contrast to S. cerevisiae genetic diversity, wild and human origin isolates were intertwined. A total of 75% of strains were proven to be homozygotes and estimated heterozygosity suggests a selfing rate above 0.95 for the different population tested here. From this point of view, the S. uvarum life cycle appears to be more closely related to S. paradoxus or S. cerevisiae of natural resources than S. cerevisiae wine isolates. Population structure could not be correlated to distinct geographic or technological origins, suggesting lower differentiation that may result from a large exchange between human and natural populations mediated by insects or human activities. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Floral diversity increases beneficial arthropod richness and decreases variability in arthropod community composition.

Science.gov (United States)

Bennett, Ashley B; Gratton, Claudio

2013-01-01

Declines in species diversity resulting from anthropogenic alterations of the environment heighten the need to develop management strategies that conserve species and ecosystem services. This study examined how native plant species and their diversity influence the abundance and richness of beneficial arthropods, a functionally important group that provides ecosystem services such as pollination and natural pest suppression. Beneficial arthropods were sampled in replicated study plots containing native perennials planted in one-, two-, and seven-species mixtures. We found plant diversity had a positive impact on arthropod richness but not on arthropod abundance. An analysis of arthropod community composition revealed that each flower species attracted a different assemblage of beneficial arthropods. In addition, the full seven-species mixture also attracted a distinct arthropod community compared to single-species monocultures. Using a multivariate approach, we determined whether arthropod assemblages in two- and seven-species plots were additive and could be predicted based on assemblages from their component single-species plots. On average, assemblages in diverse plots were nonadditive when compared to assemblages predicted using single-species plots. Arthropod assemblages in two-species plots most closely resembled those of only one of the flower species in the mixture. However, the arthropod assemblages in seven-species plots, although statistically deviating from the expectation of an additive model, more closely resembled predicted communities compared to the assemblages found in two-species plots, suggesting that variability in arthropod community composition decreased as planting diversity increased. Our study demonstrates that careful selection of plants in managed landscapes can augment beneficial arthropod richness and support a more predictable arthropod community, suggesting that planning and design efforts could shape arthropod assemblages in natural

Comparative gene expression analysis throughout the life cycle of Leishmania braziliensis: diversity of expression profiles among clinical isolates.

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Vanessa Adaui

Full Text Available BACKGROUND: Most of the Leishmania genome is reported to be constitutively expressed during the life cycle of the parasite, with a few regulated genes. Inter-species comparative transcriptomics evidenced a low number of species-specific differences related to differentially distributed genes or the differential regulation of conserved genes. It is of uppermost importance to ensure that the observed differences are indeed species-specific and not simply specific of the strains selected for representing the species. The relevance of this concern is illustrated by current study. METHODOLOGY/PRINCIPAL FINDINGS: We selected 5 clinical isolates of L. braziliensis characterized by their diversity of clinical and in vitro phenotypes. Real-time quantitative PCR was performed on promastigote and amastigote life stages to assess gene expression profiles at seven time points covering the whole life cycle. We tested 12 genes encoding proteins with roles in transport, thiol-based redox metabolism, cellular reduction, RNA poly(A-tail metabolism, cytoskeleton function and ribosomal function. The general trend of expression profiles showed that regulation of gene expression essentially occurs around the stationary phase of promastigotes. However, the genes involved in this phenomenon appeared to vary significantly among the isolates considered. CONCLUSION/SIGNIFICANCE: Our results clearly illustrate the unique character of each isolate in terms of gene expression dynamics. Results obtained on an individual strain are not necessarily representative of a given species. Therefore, extreme care should be taken when comparing the profiles of different species and extrapolating functional differences between them.

Genetic diversity, virulotyping and antimicrobial resistance susceptibility of Yersinia enterocolitica isolated from pigs and porcine products in Malaysia.

Science.gov (United States)

Thong, Kwai Lin; Tan, Lai Kuan; Ooi, Peck Toung

2018-01-01

The objectives of the present study were to determine the antimicrobial resistance, virulotypes and genetic diversity of Yersinia enterocolitica isolated from uncooked porcine food and live pigs in Malaysia. Thirty-two non-repeat Y. enterocolitica strains of three bioserotypes (3 variant/O:3, n = 27; 1B/O:8, n = 3; 1A/O:5, n = 2) were analysed. Approximately 90% of strains were multidrug-resistant with a multiple antibiotic resistance index Yersinia enterocolitica could be distinguished distinctly into three clusters by pulsed-field gel electrophoresis, with each belonging to a particular bioserotype. Strains of 3 variant/O:3 were more heterogeneous than others. Eleven of the 15 virulence genes tested (hreP, virF, rfbC, myfA, sat, inv, ail, ymoA, ystA, tccC, yadA) and pYV virulence plasmid were present in all the bioserotpe 3 variant/03 strains. The occurrence of virulent strains of Y. enterocolitica in pigs and porcine products reiterated that pigs are important reservoirs for Y. enterocolitica. The increasing trend of multidrug resistant strains is a public health concern. This is the first report on the occurrence of potential pathogenic and resistant strains of Y. enterocolitica in pigs in Malaysia. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Diversity of the subspecies Bifidobacterium animalis subsp. lactis.

Science.gov (United States)

Bunesova, Vera; Killer, Jiri; Javurkova, Barbora; Vlkova, Eva; Tejnecky, Vaclav; Musilova, Sarka; Rada, Vojtech

2017-04-01

Strains of Bifidobacterium animalis subsp. lactis are well-known health-promoting probiotics used commercially. B. animalis subsp. lactis has been isolated from different sources, and little is known about animal isolates of this taxon. The aim of this study was to examine the genotypic and phenotypic diversity between B. animalis subsp. lactis strains different animal hosts including Cameroon sheep, Barbary sheep, okapi, mouflon, German shepard and to compare to BB12, food isolates and the collection strain DSM 10140. Ten strains of B. animalis subsp. lactis from different sources were characterised by phenotyping, fingerprinting, and multilocus sequence typing (MLST). Regardless of origin, MLST and phylogenetic analyses revealed a close relationship between strains of B. animalis subsp. lactis with commercial and animal origin with the exception of isolates from ovine cheese, mouflon and German Shepard dog. Moreover, isolates from dog and mouflon showed significant differences in fermentation profiles and peptide mass fingerprints (MALDI-TOF). Results indicated phenotypic and genotypic diversity among strains of B. animalis subsp. lactis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Exoskeletons and economics: indoor arthropod diversity increases in affluent neighbourhoods.

Science.gov (United States)

Leong, Misha; Bertone, Matthew A; Bayless, Keith M; Dunn, Robert R; Trautwein, Michelle D

2016-08-01

In urban ecosystems, socioeconomics contribute to patterns of biodiversity. The 'luxury effect', in which wealthier neighbourhoods are more biologically diverse, has been observed for plants, birds, bats and lizards. Here, we used data from a survey of indoor arthropod diversity (defined throughout as family-level richness) from 50 urban houses and found that house size, surrounding vegetation, as well as mean neighbourhood income best predict the number of kinds of arthropods found indoors. Our finding, that homes in wealthier neighbourhoods host higher indoor arthropod diversity (consisting of primarily non-pest species), shows that the luxury effect can extend to the indoor environment. The effect of mean neighbourhood income on indoor arthropod diversity was particularly strong for individual houses that lacked high surrounding vegetation ground cover, suggesting that neighbourhood dynamics can compensate for local choices of homeowners. Our work suggests that the management of neighbourhoods and cities can have effects on biodiversity that can extend from trees and birds all the way to the arthropod life in bedrooms and basements. © 2016 The Authors.

Antimicrobial Susceptibilities of Geographically Diverse Clinical Human Isolates of Leptospira▿

OpenAIRE

Ressner, Roseanne A.; Griffith, Matthew E.; Beckius, Miriam L.; Pimentel, Guillermo; Miller, R. Scott; Mende, Katrin; Fraser, Susan L.; Galloway, Renee L.; Hospenthal, Duane R.; Murray, Clinton K.

2008-01-01

Although antimicrobial therapy of leptospirosis has been studied in a few randomized controlled clinical studies, those studies were limited to specific regions of the world and few have characterized infecting strains. A broth microdilution technique for the assessment of antibiotic susceptibility has been developed at Brooke Army Medical Center. In the present study, we assessed the susceptibilities of 13 Leptospira isolates (including recent clinical isolates) from Egypt, Thailand, Nicarag...

Diversity and antimicrobial activities of actinobacteria isolated from tropical mangrove sediments in Malaysia.

Science.gov (United States)

Lee, Learn-Han; Zainal, Nurullhudda; Azman, Adzzie-Shazleen; Eng, Shu-Kee; Goh, Bey-Hing; Yin, Wai-Fong; Ab Mutalib, Nurul-Syakima; Chan, Kok-Gan

2014-01-01

The aim of this study was to isolate and identify Actinobacteria from Malaysia mangrove forest and screen them for production of antimicrobial secondary metabolites. Eighty-seven isolates were isolated from soil samples collected at 4 different sites. This is the first report to describe the isolation of Streptomyces, Mycobacterium, Leifsonia, Microbacterium, Sinomonas, Nocardia, Terrabacter, Streptacidiphilus, Micromonospora, Gordonia, and Nocardioides from mangrove in east coast of Malaysia. Of 87 isolates, at least 5 isolates are considered as putative novel taxa. Nine Streptomyces sp. isolates were producing potent antimicrobial secondary metabolites, indicating that Streptomyces isolates are providing high quality metabolites for drug discovery purposes. The discovery of a novel species, Streptomyces pluripotens sp. nov. MUSC 135(T) that produced potent secondary metabolites inhibiting the growth of MRSA, had provided promising metabolites for drug discovery research. The biosynthetic potential of 87 isolates was investigated by the detection of polyketide synthetase (PKS) and nonribosomal polyketide synthetase (NRPS) genes, the hallmarks of secondary metabolites production. Results showed that many isolates were positive for PKS-I (19.5%), PKS-II (42.5%), and NRPS (5.7%) genes, indicating that mangrove Actinobacteria have significant biosynthetic potential. Our results highlighted that mangrove environment represented a rich reservoir for isolation of Actinobacteria, which are potential sources for discovery of antimicrobial secondary metabolites.

Pathotype diversity among Algerian isolates of Pyrenophora teres f. teres

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Karima BOUNGAB

2013-01-01

Full Text Available Barley Net Blotch caused by Pyrenophora teres f. teres (Ptt is one of the most important foliar diseases in north western Algeria. The disease could cause appreciable yield losses under favorable environmental conditions. Studies on pathogen variability and distribution of virulence in Ptt are essential to identify effective sources of resistance to net blotch of barley. In this study, pathogenic variability in 48 isolates of Ptt, collected from different barley-growing areas of north-western Algeria were evaluated using 22 barley genotypes as differential hosts. Trials carried out under controlled conditions confirmed the large variation in the virulence of this fungus. The genotypes exhibited variability in response ranging from complete resistance to high susceptibility. This is the first report of pathogenic variability in Ptt in north western Algeria. The 48 isolates tested were further differentiated into 12 pathotypes according to their reaction on the host. Eight differential cultivars were resistant to all isolates tested, but others were susceptible to one or more of the isolates. The variability in the pathogen and the resistance identified in some genotypes used in this study are being investigated further to develop superior, adapted germplasm for use in barley breeding programs in north western Algeria.

Increasing diversity in pediatric hematology/oncology.

Science.gov (United States)

Frugé, Ernest; Lakoski, Joan M; Luban, Naomi; Lipton, Jeffrey M; Poplack, David G; Hagey, Anne; Felgenhauer, Judy; Hilden, Joanne; Margolin, Judith; Vaiselbuh, Sarah R; Sakamoto, Kathleen M

2011-07-15

Diversity is necessary for the survival and success of both biological and social systems including societies. There is a lack of diversity, particularly the proportion of women and minorities in leadership positions, within medicine [Leadley. AAMC 2009. Steinecke and Terrell. Acad Med 2010;85:236-245]. In 2009 a group of ASPHO members recognized the need to support the career advancement of women and minority members. This article reports the results of a survey designed to characterize the comparative career pathway experience of women and minority ASPHO members. A group of ASPHO members modified a published Faculty Worklife survey [Pribbenow et al. High Educ Policy 2010;23:17-38] for use by Pediatric Hematologist-Oncologists (PHOs). A link to an online version of the survey was sent to all ASPHO members. Of 1,228 ASPHO members polled, 213 responded (17%). Women and minority PHOs reported less satisfaction than their counterparts on 70 of the 90 issues addressed in the survey including the hiring process, access to resources as well as integration and satisfaction with their organizations. Women also expressed greater dissatisfaction with issues of work-life balance, support for family obligations and personal health. The current literature suggests that there are significant disparities in career opportunities, compensation and satisfaction for women compared to men and minority compared to majority faculty in academic medicine [Nivet. J Vasc Surg 2010;51:53S-58S; Peterson et al. J Gen Intern Med 2004;19:259-265; DesRoches et al. Acad Med 2010;85:631-639; Castillo-Page. AAMC 2008]. Our data, derived from a survey of ASPHO members, suggests that this holds true for PHOs as well.

Strain-Level Diversity of Secondary Metabolism in Streptomyces albus

Science.gov (United States)

Seipke, Ryan F.

2015-01-01

Streptomyces spp. are robust producers of medicinally-, industrially- and agriculturally-important small molecules. Increased resistance to antibacterial agents and the lack of new antibiotics in the pipeline have led to a renaissance in natural product discovery. This endeavor has benefited from inexpensive high quality DNA sequencing technology, which has generated more than 140 genome sequences for taxonomic type strains and environmental Streptomyces spp. isolates. Many of the sequenced streptomycetes belong to the same species. For instance, Streptomyces albus has been isolated from diverse environmental niches and seven strains have been sequenced, consequently this species has been sequenced more than any other streptomycete, allowing valuable analyses of strain-level diversity in secondary metabolism. Bioinformatics analyses identified a total of 48 unique biosynthetic gene clusters harboured by Streptomyces albus strains. Eighteen of these gene clusters specify the core secondary metabolome of the species. Fourteen of the gene clusters are contained by one or more strain and are considered auxiliary, while 16 of the gene clusters encode the production of putative strain-specific secondary metabolites. Analysis of Streptomyces albus strains suggests that each strain of a Streptomyces species likely harbours at least one strain-specific biosynthetic gene cluster. Importantly, this implies that deep sequencing of a species will not exhaust gene cluster diversity and will continue to yield novelty. PMID:25635820

Genetic diversity of Coccidioides posadasii from Brazil.

Science.gov (United States)

Brilhante, Raimunda Sâmia Nogueira; de Lima, Rita Amanda Chaves; Ribeiro, Joyce Fonteles; de Camargo, Zoilo Pires; Castelo-Branco, Débora de Souza Collares Maia; Grangeiro, Thalles Barbosa; Cordeiro, Rossana de Aguiar; Gadelha Rocha, Marcos Fábio; Sidrim, José Júlio Costa

2013-05-01

Studies of the genetic variation within populations of Coccidioides posadasii are scarce, especially for those recovered from South America. Understanding the distribution of genotypes among populations is important for epidemiological surveillance. This study evaluated the genetic diversity of 18 Brazilian strains of C. posadasii through the sequencing of the 18-28S region of nuclear rDNA, as well as through RAPD and M13-PCR fingerprinting techniques. The sequences obtained were compared to Coccidioides spp. previously deposited in GenBank. The MEGA5 program was used to perform phylogenetic analyses. Within the C. posadasii clade, a single cluster was observed, containing seven isolates from Ceará, which presented a single nucleotide polymorphism. These isolates were from the same geographical area. The strains of C. posadasii showed a lower rate of genetic diversity in the ITS1 and ITS2 regions. The results of M13 and RAPD-PCR fingerprinting indicated a similar electrophoretic profile. No differences between clinical and environmental isolates were detected. This was the first study assessing the genetic variability of a larger number of C. posadasii isolates from Brazil.

Secular trends in Klebsiella pneumoniae isolated in a tertiary-care hospital: increasing prevalence and accelerated decline in antimicrobial susceptibility

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Rodrigo de Carvalho Santana

2016-04-01

Full Text Available Abstract: INTRODUCTION Klebsiella pneumoniae has become an increasingly important etiologic agent of nosocomial infections in recent years. This is mainly due to the expression of virulence factors and development of resistance to several antimicrobial drugs. METHODS This retrospective study examines data obtained from the microbiology laboratory of a Brazilian tertiary-care hospital. To assess temporal trends in prevalence and antimicrobial susceptibility, K. pneumoniae isolates were analyzed from 2000 to 2013. The relative frequencies of K. pneumoniae isolation were calculated among all Gram-negative bacilli isolated in each period analyzed. Susceptibility tests were performed using automated systems. RESULTS: From 2000-2006, K. pneumonia isolates comprised 10.7% of isolated Gram-negative bacilli (455/4260. From 2007-2013, this percentage was 18.1% (965/5331. Strictly considering isolates from bloodstream infections, the relative annual prevalence of K. pneumoniae increased from 14-17% to 27-32% during the same periods. A progressive decrease in K. pneumoniae susceptibility to all antimicrobial agents assessed was detected. Partial resistance was also observed to antimicrobial drugs that have been used more recently, such as colistin and tigecycline. CONCLUSIONS Our study indicates that K. pneumoniae has become a major pathogen among hospitalized patients and confirms its recent trend of increasing antimicrobial resistance.

Diversity and Antimicrobial Activities of Actinobacteria Isolated from Tropical Mangrove Sediments in Malaysia

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Learn-Han Lee

2014-01-01

Full Text Available The aim of this study was to isolate and identify Actinobacteria from Malaysia mangrove forest and screen them for production of antimicrobial secondary metabolites. Eighty-seven isolates were isolated from soil samples collected at 4 different sites. This is the first report to describe the isolation of Streptomyces, Mycobacterium, Leifsonia, Microbacterium, Sinomonas, Nocardia, Terrabacter, Streptacidiphilus, Micromonospora, Gordonia, and Nocardioides from mangrove in east coast of Malaysia. Of 87 isolates, at least 5 isolates are considered as putative novel taxa. Nine Streptomyces sp. isolates were producing potent antimicrobial secondary metabolites, indicating that Streptomyces isolates are providing high quality metabolites for drug discovery purposes. The discovery of a novel species, Streptomyces pluripotens sp. nov. MUSC 135T that produced potent secondary metabolites inhibiting the growth of MRSA, had provided promising metabolites for drug discovery research. The biosynthetic potential of 87 isolates was investigated by the detection of polyketide synthetase (PKS and nonribosomal polyketide synthetase (NRPS genes, the hallmarks of secondary metabolites production. Results showed that many isolates were positive for PKS-I (19.5%, PKS-II (42.5%, and NRPS (5.7% genes, indicating that mangrove Actinobacteria have significant biosynthetic potential. Our results highlighted that mangrove environment represented a rich reservoir for isolation of Actinobacteria, which are potential sources for discovery of antimicrobial secondary metabolites.

Endophyte microbiome diversity in micropropagated Atriplex canescens and Atriplex torreyi var griffithsii.

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Mary E Lucero

2011-03-01

Full Text Available Microbial diversity associated with micropropagated Atriplex species was assessed using microscopy, isolate culturing, and sequencing. Light, electron, and confocal microscopy revealed microbial cells in aseptically regenerated leaves and roots. Clone libraries and tag-encoded FLX amplicon pyrosequencing (TEFAP analysis amplified sequences from callus homologous to diverse fungal and bacterial taxa. Culturing isolated some seed borne endophyte taxa which could be readily propagated apart from the host. Microbial cells were observed within biofilm-like residues associated with plant cell surfaces and intercellular spaces. Various universal primers amplified both plant and microbial sequences, with different primers revealing different patterns of fungal diversity. Bacterial and fungal TEFAP followed by alignment with sequences from curated databases revealed 7 bacterial and 17 ascomycete taxa in A. canescens, and 5 bacterial taxa in A. torreyi. Additional diversity was observed among isolates and clone libraries. Micropropagated Atriplex retains a complex, intimately associated microbiome which includes diverse strains well poised to interact in manners that influence host physiology. Microbiome analysis was facilitated by high throughput sequencing methods, but primer biases continue to limit recovery of diverse sequences from even moderately complex communities.

Nitrogen deposition and management practices increase soil microbial biomass carbon but decrease diversity in Moso bamboo plantations

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Li, Quan; Song, Xinzhang; Gu, Honghao; Gao, Fei

2016-06-01

Because microbial communities play a key role in carbon (C) and nitrogen (N) cycling, changes in the soil microbial community may directly affect ecosystem functioning. However, the effects of N deposition and management practices on soil microbes are still poorly understood. We studied the effects of these two factors on soil microbial biomass carbon (MBC) and community composition in Moso bamboo plantations using high-throughput sequencing of the 16S rRNA gene. Plantations under conventional (CM) or intensive management (IM) were subjected to one of four N treatments for 30 months. IM and N addition, both separately and in combination, significantly increased soil MBC while decreasing bacterial diversity. However, increases in soil MBC were inhibited when N addition exceeded 60 kg N•ha-1•yr-1. IM increased the relative abundances of Actinobacteria and Crenarchaeota but decreased that of Acidobacteria. N addition increased the relative abundances of Acidobacteria, Crenarchaeota, and Actinobacteria but decreased that of Proteobacteria. Soil bacterial diversity was significantly related to soil pH, C/N ratio, and nitrogen and available phosphorus content. Management practices exerted a greater influence over regulation of the soil MBC and microbial diversity compared to that of N deposition in Moso bamboo plantations.

Increasing Mathematics and Science Achievement for Culturally Diverse Students through Teaching Training

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Mahon, Lee

1997-01-01

The purpose of this proposal was to field test and evaluate a Teacher Training program that would prepare teachers to increase the motivation and achievement of culturally diverse students in the areas of science and mathematics. Designed as a three year program, this report covers the first two years of the training program at the Ronald McNair School in the Ravenswood School district, using the resources of the NASA Ames Research Center and the California Framework for Mathematics and Science.

Relationship between Trypanosoma brucei rhodesiense genetic diversity and clinical spectrum among sleeping sickness patients in Uganda.

Science.gov (United States)

Kato, Charles D; Mugasa, Claire M; Nanteza, Ann; Matovu, Enock; Alibu, Vincent P

2017-10-27

Human African trypanosomiasis (HAT) due to Trypanosoma brucei rhodesiense in East and southern Africa is reported to be clinically diverse. We tested the hypothesis that this clinical diversity is associated with a variation in trypanosome genotypes. Trypanosome DNA isolated from HAT patients was genotyped using 7 microsatellite markers directly from blood spotted FTA cards following a whole genome amplification. All markers were polymorphic and identified 17 multi-locus genotypes with 56% of the isolates having replicate genotypes. We did not observe any significant clustering between isolates and bootstrap values across major tree nodes were insignificant. When genotypes were compared among patients with varying clinical presentation or outcome, replicate genotypes were observed at both extremes showing no significant association between genetic diversity and clinical outcome. Our study shows that T. b. rhodesiense isolates are homogeneous within a focus and that observed clinical diversity may not be associated with parasite genetic diversity. Other factors like host genetics and environmental factors might be involved in determining clinical diversity. Our study may be important in designing appropriate control measures that target the parasite.

Genetic Diversity and Spatial Genetic Structure of the Grassland Perennial Saxifraga granulata along Two River Systems.

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Sascha van der Meer

Full Text Available Due to changes in land use, the natural habitats of an increasing number of plant species have become more and more fragmented. In landscapes that consist of patches of suitable habitat, the frequency and extent of long-distance seed dispersal can be expected to be an important factor determining local genetic diversity and regional population structure of the remaining populations. In plant species that are restricted to riparian habitats, rivers can be expected to have a strong impact on the dynamics and spatial genetic structure of populations as they may enable long-distance seed dispersal and thus maintain gene flow between fragmented populations. In this study, we used polymorphic microsatellite markers to investigate the genetic diversity and the spatial genetic structure of 28 populations of Saxifraga granulata along two rivers in central Belgium. We hypothesized that rivers might be essential for gene flow among increasingly isolated populations of this species. Genetic diversity was high (HS = 0.68, which to a certain extent can be explained by the octoploid nature of S. granulata in the study area. Populations along the Dijle and Demer rivers were also highly differentiated (G"ST = 0.269 and 0.164 and DEST = 0.190 and 0.124, respectively and showed significant isolation-by-distance, indicating moderate levels of gene flow primarily between populations that are geographically close to each other. Along the river Demer population genetic diversity was higher upstream than downstream, suggesting that seed dispersal via the water was not the primary mode of dispersal. Overall, these results indicate that despite increasing fragmentation populations along both rivers were highly genetically diverse. The high ploidy level and longevity of S. granulata have most likely buffered negative effects of fragmentation on genetic diversity and the spatial genetic structure of populations in riparian grasslands.

Diversity and Plant Growth Promoting Proerties of Rhizobacteria ...

African Journals Online (AJOL)

The purpose of this study was to evaluate and assess the plant growth promoting characteristics and diversity of major tef rhizosphere isolates from central Ethiopia. A total of 162 bacteria were isolated from rhizosphere of tef [Eragrostis tef (Zucc.) Trotter] and characterized. While screening using some plant growth ...

Increasing student diversity and cultural competence as part of Loma Linda University School of Dentistry's service mission.

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Arnett, Margie R; Forde, Ron

2012-06-01

For many years, studies have identified a need for greater racial and ethnic diversity among dental professionals. However, the ability of the field to collectively address the problem has been hindered by the low numbers of underrepresented minority students who apply to dental school. Over the past two decades, college attendance rates have increased and U.S. dental school applications have tripled, but the number of underrepresented minority dental applicants has remained about the same. With the increasing diversity of the U.S. population and specifically that of the state of California, the dental workforce would be enhanced by the presence of more underrepresented minority dentists. Additionally, curricular changes should be implemented to better prepare dental students to meet the oral health care needs of diverse populations. There is general agreement that these workforce and curricular changes would enhance access to care for underserved populations. For seven years, Loma Linda University School of Dentistry participated in the Pipeline, Profession, and Practice: Community-Based Dental Education program. The first phase of this national program addressed deficiencies in diversity in dentistry and in access to oral health care. In the second phase, Loma Linda University continued to collaborate with other California dental schools on specific state initiatives. This article provides an overview of the school's efforts to enroll a more diverse student body, enhance all its students' cultural competence, and expand care to underserved populations.

Clonal Diversity of Chilean Isolates of Enterohemorrhagic Escherichia coli from Patients with Hemolytic-Uremic Syndrome, Asymptomatic Subjects, Animal Reservoirs, and Food Products

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Rios, Maritza; Prado, Valeria; Trucksis, Michele; Arellano, Carolina; Borie, Consuelo; Alexandre, Marcela; Fica, Alberto; Levine, Myron M.

1999-01-01

To determine clonal relationship among Chilean enterohemorrhagic Escherichia coli (EHEC) strains from different sources (clinical infections, animal reservoirs, and food), 54 EHEC isolates (44 of E. coli O157, 5 of E. coli O111, and 5 of E. coli O26) were characterized for virulence genes by colony blot hybridization and by pulsed-field gel electrophoresis (PFGE). By colony blotting, 12 different genotypes were identified among the 44 E. coli O157 isolates analyzed, of which the genetic profile stx1+ stx2+ hly+ eae+ was the most prevalent. All human O157 strains that were associated with sporadic cases of hemolytic-uremic syndrome (HUS) carried both the stx1 and stx2 toxin-encoding genes and were eaeA positive. Only 9 of 13 isolates from human controls were stx1+ stx2+, and 8 carried the eaeA gene. Comparison of profiles obtained by PFGE of XbaI-digested genomic DNA showed a great diversity among the E. coli O157 isolates, with 37 different profiles among 39 isolates analyzed. Cluster analysis of PFGE profiles showed a wide distribution of clinical isolates obtained from HUS cases and asymptomatic individuals and a clonal relationship among O157 isolates obtained from HUS cases and pigs. Analysis of virulence genes showed that a correlation exists among strains with the genotype stx1+ stx2+ eae+ and pathogenic potential. A larger difference in the PFGE restriction patterns was observed among the EHEC strains of serogroups O26 and O111. These results indicate that several different EHEC clones circulate in Chile and suggest that pigs are an important animal reservoir for human infections by EHEC. Guidelines have been proposed for better practices in the slaughter of animals in Chile. PMID:9986852

Enduring increases in anxiety-like behavior and rapid nucleus accumbens dopamine signaling in socially isolated rats.

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Yorgason, Jordan T; España, Rodrigo A; Konstantopoulos, Joanne K; Weiner, Jeffrey L; Jones, Sara R

2013-03-01

Social isolation (SI) rearing, a model of early life stress, results in profound behavioral alterations, including increased anxiety-like behavior, impaired sensorimotor gating and increased self-administration of addictive substances. These changes are accompanied by alterations in mesolimbic dopamine function, such as increased dopamine and metabolite tissue content, increased dopamine responses to cues and psychostimulants, and increased dopamine neuron burst firing. Using voltammetric techniques, we examined the effects of SI rearing on dopamine transporter activity, vesicular release and dopamine D2-type autoreceptor activity in the nucleus accumbens core. Long-Evans rats were housed in group (GH; 4/cage) or SI (1/cage) conditions from weaning into early adulthood [postnatal day (PD) 28-77]. After this initial housing period, rats were assessed on the elevated plus-maze for an anxiety-like phenotype, and then slice voltammetry experiments were performed. To study the enduring effects of SI rearing on anxiety-like behavior and dopamine terminal function, another cohort of similarly reared rats was isolated for an additional 4 months (until PD 174) and then tested. Our findings demonstrate that SI rearing results in lasting increases in anxiety-like behavior, dopamine release and dopamine transporter activity, but not D2 activity. Interestingly, GH-reared rats that were isolated as adults did not develop the anxiety-like behavior or dopamine changes seen in SI-reared rats. Together, our data suggest that early life stress results in an anxiety-like phenotype, with lasting increases in dopamine terminal function. © 2013 Federation of European Neuroscience Societies and Blackwell Publishing Ltd.

Isolation and characterization of biosurfactant producing bacteria from Persian Gulf (Bushehr provenance)

International Nuclear Information System (INIS)

Hassanshahian, Mehdi

2014-01-01

Highlights: • Biosurfactant producing bacteria were isolated from Persian Gulf. • There is high diversity of biosurfactant producing bacteria in the Persian Gulf. • These bacteria are very useful for management of oil pollution in the sea. - Abstract: Biosurfactants are surface active materials that are produced by some microorganisms. These molecules increase biodegradation of insoluble pollutants. In this study sediments and seawater samples were collected from the coastline of Bushehr provenance in the Persian Gulf and their biosurfactant producing bacteria were isolated. Biosurfactant producing bacteria were isolated by using an enrichment method in Bushnell-Hass medium with diesel oil as the sole carbon source. Five screening tests were used for selection of Biosurfactant producing bacteria: hemolysis in blood agar, oil spreading, drop collapse, emulsification activity and Bacterial Adhesion to Hydrocarbon test (BATH). These bacteria were identified using biochemical and molecular methods. Eighty different colonies were isolated from the collected samples. The most biosurfactant producing isolates related to petrochemical plants of Khark Island. Fourteen biosurfactant producing bacteria were selected between these isolates and 7 isolates were screened as these were predominant producers that belong to Shewanella alga, Shewanella upenei, Vibrio furnissii, Gallaecimonas pentaromativorans, Brevibacterium epidermidis, Psychrobacter namhaensis and Pseudomonas fluorescens. The largest clear zone diameters in oil spreading were observed for G. pentaromativorans strain O15. Also, this strain has the best emulsification activity and reduction of surface tension, suggesting it is the best of thee isolated strains. The results of this study confirmed that there is high diversity of biosurfactant producing bacteria in marine ecosystem of Iran and by application of these bacteria in petrochemical waste water environmental problems can be assisted

Natural product diversity of actinobacteria in the Atacama Desert.

Science.gov (United States)

Rateb, Mostafa E; Ebel, Rainer; Jaspars, Marcel

2018-02-14

The Atacama Desert of northern Chile is considered one of the most arid and extreme environment on Earth. Its core region was described as featuring "Mars-like" soils that were at one point deemed too extreme for life to exist. However, recent investigations confirmed the presence of diverse culturable actinobacteria. In the current review, we discuss a total of 46 natural products isolated to date representing diverse chemical classes characterized from different actinobacteria isolated from various locations in the Atacama Desert. Their reported biological activities are also discussed.

Increasing Scientific Literacy at Minority Serving Institutions Nationwide through AMS Professional Development Diversity Workshops

Science.gov (United States)

Brey, J. A.; Geer, I. W.; Mills, E. W.; Nugnes, K. A.; Moses, M. N.

2011-12-01

Increasing students' earth science literacy, especially those at Minority Serving Institutions (MSIs), is a primary goal of the American Meteorological Society (AMS). Through the NSF-supported AMS Weather Studies and AMS Ocean Studies Diversity workshops for Historically Black College and Universities, Hispanic Serving Institutions, Tribal Colleges and Universities, Alaska Native, and Native Hawaiian Serving Institutions, AMS has brought meteorology and oceanography courses to more students. These workshops trained and mentored faculty implementing AMS Weather Studies and AMS Ocean Studies. Of the 145 institutions that have participated in the AMS Weather Studies Diversity Project, reaching over 13,000 students, it was the first meteorology course offered for more than two-thirds of the institutions. As a result of the AMS Ocean Studies Diversity Project, 75 institutions have offered the course to more than 3000 students. About 50 MSIs implemented both the Weather and Ocean courses, improving the Earth Science curriculum on their campuses. With the support of NSF and NASA, and a partnership with Second Nature, the organizing entity behind the American College and University President's Climate Commitment (ACUPCC), the newest professional development workshop, AMS Climate Studies Diversity Project will recruit MSI faculty members through the vast network of Second Nature's more than 670 signatories. These workshops will begin in early summer 2012. An innovative approach to studying climate science, AMS Climate Studies explores the fundamental science of Earth's climate system and addresses the societal impacts relevant to today's students and teachers. The course utilizes resources from respected organizations, such as the IPCC, the US Global Change Research Program, NASA, and NOAA. In addition, faculty and students learn about basic climate modeling through the AMS Conceptual Energy Model. Following the flow of energy in a clear, simplified model from space to

Pathotypic diversity of Rhynchosporium secalis (Oudem) in Tunisia ...

African Journals Online (AJOL)

Pathotypic diversity was high, with 93 R. secalis pathotypes identified on two differential sets (one comprising 9 and the other 10 barley lines) containing known resistance genes. A few pathotypes comprised 2% of the isolates; however, the majorities were represented by a single isolate. None of the differential lines was ...

Response diversity can increase ecological resilience to disturbance in coral reefs.

Science.gov (United States)

Baskett, Marissa L; Fabina, Nicholas S; Gross, Kevin

2014-08-01

Community-level resilience depends on the interaction between multiple populations that vary in individual responses to disturbance. For example, in tropical reefs, some corals can survive higher stress (resistance) while others exhibit faster recovery (engineering resilience) following disturbances such as thermal stress. While each type will negatively affect the other through competition, each might also benefit the other by reducing the potential for an additional competitor such as macroalgae to invade after a disturbance. To determine how community composition affects ecological resilience, we modeled coral-macroalgae interactions given either a resistant coral, a resilient coral, or both together. Having both coral types (i.e., response diversity) can lead to observable enhanced ecological resilience if (1) the resilient coral is not a superior competitor and (2) disturbance levels are high enough such that the resilient coral would collapse when considered alone. This enhanced resilience occurs through competitor-enabled rescue where each coral increases the potential for the other to recover from disturbance through external recruitment, such that both corals benefit from the presence of each other in terms of total cover and resilience. Therefore, conservation management aimed at protecting resilience under global change requires consideration of both diversity and connectivity between sites experiencing differential disturbance.

Genetic diversity and species diversity of stream fishes covary across a land-use gradient

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Blum, M.J.; Bagley, M.J.; Walters, D.M.; Jackson, S.A.; Daniel, F.B.; Chaloud, D.J.; Cade, B.S.

2012-01-01

Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems. ?? 2011 Springer-Verlag.

Revegetation increase bird diversity in coastal area of Socorejo, Tuban, East Java - Indonesia

Science.gov (United States)

Lestari, Yeni Indah; Edi, Wasito; Alivvy, Alkautsar; Ibadah, Acib Setia; Sari, Fadina Yuliana; Nuraini, Finda; Yanuar, Ahmad; Satriyono, Agus; Riany, Citra Fitrie; Saptarini, Dian; Muzaki, Farid Kamal

2017-06-01

Study to address positive impact of revegetation program to increasing diversity of bird had been conducted in coastal area of Socorejo, Tuban - Indonesia. Field observation conducted during April 2011 (representing pre-revegetation period), April 2015 and May 2016 (representing post-revegetation period). A belt transect (500 meter long and 50 meter width) was used to survey the abundance and species composition of birds community. In general, we identified at least 51 bird species from three observation times. From 2011 to 2016, the numbers of the birds identified are 23, 37 and 37 species; while the Shannon-Wiener diversity indices (H') are 1.865, 2.071 and 2.957, respectively. In addition, there are 11 national or internationally protected species, 3 Indonesian endemic species and 12 migratory species occurred in the area. As a conclusion, the coastal revegetation program provides positive impact by generating habitat function for bird community.

Increased Mitochondrial Genetic Diversity in Persons Infected With Hepatitis C VirusSummary

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David S. Campo

2016-09-01

Full Text Available Background & Aims: The host genetic environment contributes significantly to the outcomes of hepatitis C virus (HCV infection and therapy response, but little is known about any effects of HCV infection on the host beyond any changes related to adaptive immune responses. HCV persistence is associated strongly with mitochondrial dysfunction, with liver mitochondrial DNA (mtDNA genetic diversity linked to disease progression. Methods: We evaluated the genetic diversity of 2 mtDNA genomic regions (hypervariable segments 1 and 2 obtained from sera of 116 persons using next-generation sequencing. Results: Results were as follows: (1 the average diversity among cases with seronegative acute HCV infection was 4.2 times higher than among uninfected controls; (2 the diversity level among cases with chronic HCV infection was 96.1 times higher than among uninfected controls; and (3 the diversity was 23.1 times higher among chronic than acute cases. In 2 patients who were followed up during combined interferon and ribavirin therapy, mtDNA nucleotide diversity decreased dramatically after the completion of therapy in both patients: by 100% in patient A after 54 days and by 70.51% in patient B after 76 days. Conclusions: HCV infection strongly affects mtDNA genetic diversity. A rapid decrease in mtDNA genetic diversity observed after therapy-induced HCV clearance suggests that the effect is reversible, emphasizing dynamic genetic relationships between HCV and mitochondria. The level of mtDNA nucleotide diversity can be used to discriminate recent from past infections, which should facilitate the detection of recent transmission events and thus help identify modes of transmission. Keywords: Disease Biomarkers, mtDNA, Noninvasive

Genetic diversity and pectinolytic activity of epiphytic yeasts from grape carposphere.

Science.gov (United States)

Filho, M Cilião; Bertéli, M B D; Valle, J S; Paccola-Meirelles, L D; Linde, G A; Barcellos, F G; Colauto, N B

2017-06-20

The genetic diversity of epiphytic yeasts from grape carposphere is susceptible to environmental variations that determine the predominant carposphere microbiota. Understanding the diversity of yeasts that inhabit grape carposphere in different environments and their pectinolytic activity is a way to understand the biotechnological potential that surrounds us and help improve winemaking. Therefore, this study aimed to evaluate the pectinolytic activity and characterize the genetic diversity of isolated epiphytic yeasts from grape carposphere. Grapes of the Bordeaux cultivar were collected from different regions of Paraná and Rio Grande do Sul States, in Brazil, and the yeasts were isolated from these grape carpospheres. Monosporic isolates were morphologically and genetically characterized on potato dextrose agar medium and by PCR-RFLP and rep-PCR (BOX-PCR) in the ITS1-5.8S-ITS2 region of rDNA. The index of pectinolytic activity of isolates was also evaluated estimating the ratio between the halo diameter of enzymatic degradation and the diameter of the colony when the isolates were grown in cultivation medium containing 10 g/L pectin, 5 g/L yeast extract, 15 g/L agar, 0.12% (w/v) Congo red, and pH 6.2. We observed that the grape carposphere is an environment with a great genetic diversity of epiphytic yeasts of the following genera: Cryptococcus (31.25%), Pichia (25.0%), Candida (25.0%), Dekkera (12.5%), and Saccharomyces (6.25%). The PCR-RFLP technique allowed analyzing existing polymorphism among individuals of a population based on a more restrict and evolutionarily preserved region, mostly utilized to differentiate isolates at the genus level. Approximately 33% of yeast isolates presented pectinolytic activity with potential biotechnological for wine and fruit juice production. This great genetic variability found indicated that it is a potential reservoir of genes to be applied in viniculture improvement programs.

Diversity of β-lactamases produced by imipenem resistant, Pseudomonas aeruginosa isolates from the bloodstream.

Science.gov (United States)

Najar Peerayeh, Shahin; Pirhajati Mahabadi, Rahim; Pakbaten Toupkanlou, Sanaz; Siadat, Seyed Davar

2014-11-01

The emergence of imipenem non-susceptible Pseudomonas aeruginosa isolates is a matter of great concern because these isolates can become resistant to all available antibiotics. This study conducted to characterize β-lactamase genes in imipenem resistant P. aeruginosa isolates from bloodstream. 56 non-duplicate clinical isolates of P. aeruginosa were collected in Tehran hospitals. Antibacterial susceptibility was determined by disk diffusion and MIC methods. ESBL and MBL production was confirmed by combined disk. β-Lactamase classes A, B and D genes were identified by PCR. Seventeen (30.3%) isolates were imipenem resistant for which 16 isolates simultaneously were resistant to all tested antibiotics. While among 39 imipenem susceptible isolates, only two isolates were resistant to all tested antibiotics. In imipenem resistant isolates, blaTEM, blaSHV and blaOXA-10 were found in 41.1% of isolates and blaVIM, blaIMP and blaPER were identified in 47%, 11.7% and 5.8% of isolates respectively, while in imipenem susceptible isolates, blaTEM, blaSHV and blaOXA-10 were determined in 2.5%, 7.6% and 33.3% of isolates, respectively. The imipenem resistant isolates had been recovered mostly (67.7%) from patients in the Burn hospital. The result of this study indicated the emergence of multidrug resistant MBL and non-MBL producing P. aeruginosa, particularly in the Burn hospital and blaVIM was dominant β-lactamase genes in imipenem resistant isolates. The isolation of carrier patients may lead to prevent a further dissemination. Copyright © 2014 Elsevier Ltd and ISBI. All rights reserved.

Ongoing Horizontal and Vertical Transmission of Virulence Genes and papA Alleles among Escherichia coli Blood Isolates from Patients with Diverse-Source Bacteremia

Science.gov (United States)

Johnson, James R.; O'Bryan, Timothy T.; Kuskowski, Michael; Maslow, Joel N.

2001-01-01

The phylogenetic distributions of multiple putative virulence factors (VFs) and papA (P fimbrial structural subunit) alleles among 182 Escherichia coli blood isolates from patients with diverse-source bacteremia were defined. Phylogenetic correspondence among these strains, the E. coli Reference (ECOR) collection, and other collections of extraintestinal pathogenic E. coli (ExPEC) was assessed. Although among the 182 bacteremia isolates phylogenetic group B2 predominated, exhibited the greatest concentration of individual VFs, and contained the largest number of familiar virulent clones, other phylogenetic groups exhibited greater concentrations of certain VFs than did group B2 and included several additional virulent clones. Certain of the newly detected VF genes, e.g., fyuA (yersiniabactin; 76%) and focG (F1C fimbriae; 25%), were as prevalent or more prevalent than their more familiar traditional counterparts, e.g., iut (aerobactin; 57%) and sfaS (S fimbriae; 14%), thus possibly offering additional useful targets for preventive interventions. Considerable diversity of VF profiles was observed at every level within the phylogenetic tree, including even within individual lineages. This suggested that many different pathways can lead to extraintestinal virulence in E. coli and that the evolution of ExPEC, which involves extensive horizontal transmission of VFs and continuous remodeling of pathogenicity-associated islands, is a highly active, ongoing process. PMID:11500406

Early Life Stress Increases Metabolic Risk, HPA Axis Reactivity, and Depressive-Like Behavior When Combined with Postweaning Social Isolation in Rats.

Science.gov (United States)

Vargas, Javier; Junco, Mariana; Gomez, Carlos; Lajud, Naima

2016-01-01

Early-life stress is associated with depression and metabolic abnormalities that increase the risk of cardiovascular disease and diabetes. Such associations could be due to increased glucocorticoid levels. Periodic maternal separation in the neonate and rearing in social isolation are potent stressors that increase hypothalamus-pituitary-adrenal axis activity. Moreover, social isolation promotes feed intake and body weight gain in rats subjected to periodic maternal separation; however, its effects on metabolic risks have not been described. In the present study, we evaluated whether periodic maternal separation, social isolation rearing, and a combination of these two stressors (periodic maternal separation + social isolation rearing) impair glucose homeostasis and its relation to the hypothalamus-pituitary-adrenal axis and depressive-like behavior. Periodic maternal separation increased basal corticosterone levels, induced a passive coping strategy in the forced swimming test, and was associated with a mild (24%) increase in fasting glucose, insulin resistance, and dyslipidemia. Rearing in social isolation increased stress reactivity in comparison to both controls and in combination with periodic maternal separation, without affecting the coping strategy associated with the forced swimming test. However, social isolation also increased body weight gain, fasting glucose (120%), and insulin levels in rats subjected to periodic maternal separation. Correlation analyses showed that stress-induced effects on coping strategy on the forced swimming test (but not on metabolic risk markers) are associated with basal corticosterone levels. These findings suggest that maternal separation and postweaning social isolation affect stress and metabolic vulnerability differentially and that early-life stress-related effects on metabolism are not directly dependent on glucocorticoid levels. In conclusion, our study supports the cumulative stress hypothesis, which suggests that

A Compact UWB Diversity Antenna

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Hui Zhao

2014-01-01

Full Text Available A compact printed ultrawideband (UWB diversity antenna with a size of 30 mm × 36 mm operating at a frequency range of 3.1–10.6 GHz is proposed. The antenna is composed of two semielliptical monopoles fed by two microstrip lines. Two semicircular slots, two rectangular slots, and one stub are introduced in the ground plane to adjust the impedance bandwidth of the antenna and improve the isolation between two feeding ports. The simulated and measured results show that impedance bandwidth of the proposed antenna can cover the whole UWB band with a good isolation of < −15 dB. The radiation patterns, peak antenna gain, and envelope correlation coefficient are also measured and discussed. The measured results show that the proposed antenna can be a good candidate for some portable MIMO/diversity UWB applications.

Elevated Genetic Diversity in the Emerging Blueberry Pathogen Exobasidium maculosum.

Science.gov (United States)

Stewart, Jane E; Brooks, Kyle; Brannen, Phillip M; Cline, William O; Brewer, Marin T

2015-01-01

Emerging diseases caused by fungi are increasing at an alarming rate. Exobasidium leaf and fruit spot of blueberry, caused by the fungus Exobasidium maculosum, is an emerging disease that has rapidly increased in prevalence throughout the southeastern USA, severely reducing fruit quality in some plantings. The objectives of this study were to determine the genetic diversity of E. maculosum in the southeastern USA to elucidate the basis of disease emergence and to investigate if populations of E. maculosum are structured by geography, host species, or tissue type. We sequenced three conserved loci from 82 isolates collected from leaves and fruit of rabbiteye blueberry (Vaccinium virgatum), highbush blueberry (V. corymbosum), and southern highbush blueberry (V. corymbosum hybrids) from commercial fields in Georgia and North Carolina, USA, and 6 isolates from lowbush blueberry (V. angustifolium) from Maine, USA, and Nova Scotia, Canada. Populations of E. maculosum from the southeastern USA and from lowbush blueberry in Maine and Nova Scotia are distinct, but do not represent unique species. No difference in genetic structure was detected between different host tissues or among different host species within the southeastern USA; however, differentiation was detected between populations in Georgia and North Carolina. Overall, E. maculosum showed extreme genetic diversity within the conserved loci with 286 segregating sites among the 1,775 sequenced nucleotides and each isolate representing a unique multilocus haplotype. However, 94% of the nucleotide substitutions were silent, so despite the high number of mutations, selective constraints have limited changes to the amino acid sequences of the housekeeping genes. Overall, these results suggest that the emergence of Exobasidium leaf and fruit spot is not due to a recent introduction or host shift, or the recent evolution of aggressive genotypes of E. maculosum, but more likely as a result of an increasing host population

Elevated Genetic Diversity in the Emerging Blueberry Pathogen Exobasidium maculosum

Science.gov (United States)

Stewart, Jane E.; Brooks, Kyle; Brannen, Phillip M.; Cline, William O.; Brewer, Marin T.

2015-01-01

Emerging diseases caused by fungi are increasing at an alarming rate. Exobasidium leaf and fruit spot of blueberry, caused by the fungus Exobasidium maculosum, is an emerging disease that has rapidly increased in prevalence throughout the southeastern USA, severely reducing fruit quality in some plantings. The objectives of this study were to determine the genetic diversity of E. maculosum in the southeastern USA to elucidate the basis of disease emergence and to investigate if populations of E. maculosum are structured by geography, host species, or tissue type. We sequenced three conserved loci from 82 isolates collected from leaves and fruit of rabbiteye blueberry (Vaccinium virgatum), highbush blueberry (V. corymbosum), and southern highbush blueberry (V. corymbosum hybrids) from commercial fields in Georgia and North Carolina, USA, and 6 isolates from lowbush blueberry (V. angustifolium) from Maine, USA, and Nova Scotia, Canada. Populations of E. maculosum from the southeastern USA and from lowbush blueberry in Maine and Nova Scotia are distinct, but do not represent unique species. No difference in genetic structure was detected between different host tissues or among different host species within the southeastern USA; however, differentiation was detected between populations in Georgia and North Carolina. Overall, E. maculosum showed extreme genetic diversity within the conserved loci with 286 segregating sites among the 1,775 sequenced nucleotides and each isolate representing a unique multilocus haplotype. However, 94% of the nucleotide substitutions were silent, so despite the high number of mutations, selective constraints have limited changes to the amino acid sequences of the housekeeping genes. Overall, these results suggest that the emergence of Exobasidium leaf and fruit spot is not due to a recent introduction or host shift, or the recent evolution of aggressive genotypes of E. maculosum, but more likely as a result of an increasing host population

Elevated Genetic Diversity in the Emerging Blueberry Pathogen Exobasidium maculosum.

Directory of Open Access Journals (Sweden)

Jane E Stewart

Full Text Available Emerging diseases caused by fungi are increasing at an alarming rate. Exobasidium leaf and fruit spot of blueberry, caused by the fungus Exobasidium maculosum, is an emerging disease that has rapidly increased in prevalence throughout the southeastern USA, severely reducing fruit quality in some plantings. The objectives of this study were to determine the genetic diversity of E. maculosum in the southeastern USA to elucidate the basis of disease emergence and to investigate if populations of E. maculosum are structured by geography, host species, or tissue type. We sequenced three conserved loci from 82 isolates collected from leaves and fruit of rabbiteye blueberry (Vaccinium virgatum, highbush blueberry (V. corymbosum, and southern highbush blueberry (V. corymbosum hybrids from commercial fields in Georgia and North Carolina, USA, and 6 isolates from lowbush blueberry (V. angustifolium from Maine, USA, and Nova Scotia, Canada. Populations of E. maculosum from the southeastern USA and from lowbush blueberry in Maine and Nova Scotia are distinct, but do not represent unique species. No difference in genetic structure was detected between different host tissues or among different host species within the southeastern USA; however, differentiation was detected between populations in Georgia and North Carolina. Overall, E. maculosum showed extreme genetic diversity within the conserved loci with 286 segregating sites among the 1,775 sequenced nucleotides and each isolate representing a unique multilocus haplotype. However, 94% of the nucleotide substitutions were silent, so despite the high number of mutations, selective constraints have limited changes to the amino acid sequences of the housekeeping genes. Overall, these results suggest that the emergence of Exobasidium leaf and fruit spot is not due to a recent introduction or host shift, or the recent evolution of aggressive genotypes of E. maculosum, but more likely as a result of an increasing

First report of cyanobacterial diversity and microcystins in a ...

African Journals Online (AJOL)

The cyanobacterial diversity of Sidi Boughaba, a Moroccan coastal lagoon and Ramsar site, was evaluated and its potentially toxic species were isolated and characterised. This study was the first time that cyanobacterial diversity and cyanotoxin production have been characterised in a Moroccan coastal lagoon. Samples ...

Genotype and Phenotype Characterization of Indonesian Phytophthora infestans Isolates Collected From Java and Outside Java Island

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Dwinita Wikan Utami

2017-10-01

Full Text Available Phytophthora infestans, the cause of late blight disease, is a worldwide problem in potato and tomato production. To understand the biology and ecology of P. infestans and the mechanism of spatial and temporal factors for the variation in P. infestans, the population diversity is required to be fully characterized. The objective of this research is to characterize the diversity of P. infestans. Surveys and collection of P. infestans isolates were performed on many locations of potato's production center in Indonesia, as in Java (West Java, Central Java, and East Java and outside of Java islands (Medan, Jambi, and Makassar. The collected isolates were then analyzed for their virulence diversity via plant disease bioassays on differential varieties and genotype diversity based on fragment analysis genotypes profile using the multiplexing 20 simple sequence repeat markers. The virulence characterization showed that the isolates group from Makassar, South Sulawesi, have the broad spectrum virulence pathotype to R1, R2, R3, R4, and R5 differential plants. Simple sequence repeat genotype characterization showed that in general, the population structure of P. infestans grouping is accordance to the origin of the sampling locations. The diversity between populations is lower than diversity between isolates in one location population groups. The characters of P. infestans population showed that the population diversity of P. infestans more occurs on individual isolates in one location compared with the diversity between the population location sampling.

Pharmacological Potential of Phylogenetically Diverse Actinobacteria Isolated from Deep-Sea Coral Ecosystems of the Submarine Avilés Canyon in the Cantabrian Sea.

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Sarmiento-Vizcaíno, Aida; González, Verónica; Braña, Alfredo F; Palacios, Juan J; Otero, Luis; Fernández, Jonathan; Molina, Axayacatl; Kulik, Andreas; Vázquez, Fernando; Acuña, José L; García, Luis A; Blanco, Gloria

2017-02-01

Marine Actinobacteria are emerging as an unexplored source for natural product discovery. Eighty-seven deep-sea coral reef invertebrates were collected during an oceanographic expedition at the submarine Avilés Canyon (Asturias, Spain) in a range of 1500 to 4700 m depth. From these, 18 cultivable bioactive Actinobacteria were isolated, mainly from corals, phylum Cnidaria, and some specimens of phyla Echinodermata, Porifera, Annelida, Arthropoda, Mollusca and Sipuncula. As determined by 16S rRNA sequencing and phylogenetic analyses, all isolates belong to the phylum Actinobacteria, mainly to the Streptomyces genus and also to Micromonospora, Pseudonocardia and Myceligenerans. Production of bioactive compounds of pharmacological interest was investigated by high-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS) techniques and subsequent database comparison. Results reveal that deep-sea isolated Actinobacteria display a wide repertoire of secondary metabolite production with a high chemical diversity. Most identified products (both diffusible and volatiles) are known by their contrasted antibiotic or antitumor activities. Bioassays with ethyl acetate extracts from isolates displayed strong antibiotic activities against a panel of important resistant clinical pathogens, including Gram-positive and Gram-negative bacteria, as well as fungi, all of them isolated at two main hospitals (HUCA and Cabueñes) from the same geographical region. The identity of the active extracts components of these producing Actinobacteria is currently being investigated, given its potential for the discovery of pharmaceuticals and other products of biotechnological interest.

Effectiveness of Arbuscular Mycorrhizal Fungal Isolates from the Land Uses of Amazon Region in Symbiosis with Cowpea.

Science.gov (United States)

Silva, Gláucia Alves E; Siqueira, José O; Stürmer, Sidney L; Moreira, Fatima M S

2018-01-01

Arbuscular mycorrhizal fungi provide several ecosystem services, including increase in plant growth and nutrition. The occurrence, richness, and structure of arbuscular mycorrhizal fungi communities are influenced by human activities, which may affect the functional benefits of these components of the soil biota. In this study, 13 arbuscular mycorrhizal fungi isolates originating from soils with different land uses in the Alto Solimões-Amazon region were evaluated regarding their effect on growth, nutrition, and cowpea yield in controlled conditions using two soils. Comparisons with reference isolates and a mixture of isolates were also performed. Fungal isolates exhibited a wide variability associated with colonization, sporulation, production of aboveground biomass, nitrogen and phosphorus uptake, and grain yield, indicating high functional diversity within and among fungal species. A generalized effect of isolates in promoting phosphorus uptake, increase in biomass, and cowpea yield was observed in both soils. The isolates of Glomus were the most efficient and are promising isolates for practical inoculation programs. No relationship was found between the origin of fungal isolate (i.e. land use) and their symbiotic performance in cowpea.

Diversity and antibiotic resistance patterns of Sphingomonadaceae isolates from drinking water.

Science.gov (United States)

Vaz-Moreira, Ivone; Nunes, Olga C; Manaia, Célia M

2011-08-15

Sphingomonadaceae (n = 86) were isolated from a drinking water treatment plant (n = 6), tap water (n = 55), cup fillers for dental chairs (n = 21), and a water demineralization filter (n = 4). The bacterial isolates were identified based on analysis of the 16S rRNA gene sequence, and intraspecies variation was assessed on the basis of atpD gene sequence analysis. The isolates were identified as members of the genera Sphingomonas (n = 27), Sphingobium (n = 28), Novosphingobium (n = 12), Sphingopyxis (n = 7), and Blastomonas (n = 12). The patterns of susceptibility to five classes of antibiotics were analyzed and compared for the different sites of isolation and taxonomic groups. Colistin resistance was observed to be intrinsic (92%). The highest antibiotic resistance prevalence values were observed in members of the genera Sphingomonas and Sphingobium and for beta-lactams, ciprofloxacin, and cotrimoxazole. In tap water and in water from dental chairs, antibiotic resistance was more prevalent than in the other samples, mainly due to the predominance of isolates of the genera Sphingomonas and Sphingobium. These two genera presented distinct patterns of association with antibiotic resistance, suggesting different paths of resistance development. Antibiotic resistance patterns were often related to the species rather than to the site or strain, suggesting the importance of vertical resistance transmission in these bacteria. This is the first study demonstrating that members of the family Sphingomonadaceae are potential reservoirs of antibiotic resistance in drinking water.

Diversity and Antibiotic Resistance Patterns of Sphingomonadaceae Isolates from Drinking Water▿

Science.gov (United States)

Vaz-Moreira, Ivone; Nunes, Olga C.; Manaia, Célia M.

2011-01-01

Sphingomonadaceae (n = 86) were isolated from a drinking water treatment plant (n = 6), tap water (n = 55), cup fillers for dental chairs (n = 21), and a water demineralization filter (n = 4). The bacterial isolates were identified based on analysis of the 16S rRNA gene sequence, and intraspecies variation was assessed on the basis of atpD gene sequence analysis. The isolates were identified as members of the genera Sphingomonas (n = 27), Sphingobium (n = 28), Novosphingobium (n = 12), Sphingopyxis (n = 7), and Blastomonas (n = 12). The patterns of susceptibility to five classes of antibiotics were analyzed and compared for the different sites of isolation and taxonomic groups. Colistin resistance was observed to be intrinsic (92%). The highest antibiotic resistance prevalence values were observed in members of the genera Sphingomonas and Sphingobium and for beta-lactams, ciprofloxacin, and cotrimoxazole. In tap water and in water from dental chairs, antibiotic resistance was more prevalent than in the other samples, mainly due to the predominance of isolates of the genera Sphingomonas and Sphingobium. These two genera presented distinct patterns of association with antibiotic resistance, suggesting different paths of resistance development. Antibiotic resistance patterns were often related to the species rather than to the site or strain, suggesting the importance of vertical resistance transmission in these bacteria. This is the first study demonstrating that members of the family Sphingomonadaceae are potential reservoirs of antibiotic resistance in drinking water. PMID:21705522

Rapid Isolation and Molecular Detection of Streptomycin-Producing Streptomycetes

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M Motovali-bashi

2006-07-01

Full Text Available Introduction: Streptomyces species are mycelial, aerobic gram-positive bacteria that are isolated from soil and produce a diverse range of antibiotics. Streptomyces griseus produces the antibiotic, streptomycin and forms spores even in a liquid culture. The gene cluster for the production of Streptomycin antibiotic contains strR gene that encodes StrR, a pathway-specific regulator. Then, this pathway-specific regulator induces transcription of other streptomycin production genes in the gene cluster. The overall aim of this work was rapid isolation and molecular detection of streptomycin-producing Streptomycetes, especially S. griseus, from Iranian soils in order to manipulate them for increased production of streptomycin. Methods: This research used new initiative half-specific medium for isolation of Streptomycetes from natural environments, called FZmsn. The fifty colonies of Streptomyces strains grown on the surface of FZmsn medium isolated from environmental samples were defined on the basis of their morphological characteristics and light microscope studies. A set of primers was designed to detect strR by OLIGO software. Results: In colony-PCR reactions followed by gel electrophoresis, 6 colonies from Streptomyces strains colonies were detected as S. griseus colonies. Conclusion: These native Streptomyces strains will be used for genetic manipulation of S. griseus in order to increase production levels of streptomycin.

Litter-forager termite mounds enhance the ectomycorrhizal symbiosis between Acacia holosericea A. Cunn. Ex G. Don and Scleroderma dictyosporum isolates.

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Duponnois, Robin; Assikbetse, Komi; Ramanankierana, Heriniaina; Kisa, Marija; Thioulouse, Jean; Lepage, Michel

2006-05-01

The hypothesis of the present study was that the termite mounds of Macrotermes subhyalinus (MS) (a litter-forager termite) were inhabited by a specific microflora that could enhance with the ectomycorrhizal fungal development. We tested the effect of this feeding group mound material on (i) the ectomycorrhization symbiosis between Acacia holosericea (an Australian Acacia introduced in the sahelian areas) and two ectomycorrhizal fungal isolates of Scleroderma dictyosporum (IR408 and IR412) in greenhouse conditions, (ii) the functional diversity of soil microflora and (iii) the diversity of fluorescent pseudomonads. The results showed that the termite mound amendment significantly increased the ectomycorrhizal expansion. MS mound amendment and ectomycorrhizal inoculation induced strong modifications of the soil functional microbial diversity by promoting the multiplication of carboxylic acid catabolizing microorganisms. The phylogenetic analysis showed that fluorescent pseudomonads mostly belong to the Pseudomonads monteillii species. One of these, P. monteillii isolate KR9, increased the ectomycorrhizal development between S. dictyosporum IR412 and A. holosericea. The occurrence of MS termite mounds could be involved in the expansion of ectomycorrhizal symbiosis and could be implicated in nutrient flow and local diversity.

Voluntary locomotor activity mitigates oxidative damage associated with isolation stress in the prairie vole (Microtus ochrogaster).

Science.gov (United States)

Fletcher, Kelsey L; Whitley, Brittany N; Treidel, Lisa A; Thompson, David; Williams, Annie; Noguera, Jose C; Stevenson, Jennie R; Haussmann, Mark F

2015-07-01

Organismal performance directly depends on an individual's ability to cope with a wide array of physiological challenges. For social animals, social isolation is a stressor that has been shown to increase oxidative stress. Another physiological challenge, routine locomotor activity, has been found to decrease oxidative stress levels. Because we currently do not have a good understanding of how diverse physiological systems like stress and locomotion interact to affect oxidative balance, we studied this interaction in the prairie vole (Microtus ochrogaster). Voles were either pair housed or isolated and within the isolation group, voles either had access to a moving wheel or a stationary wheel. We found that chronic periodic isolation caused increased levels of oxidative stress. However, within the vole group that was able to run voluntarily, longer durations of locomotor activity were associated with less oxidative stress. Our work suggests that individuals who demonstrate increased locomotor activity may be better able to cope with the social stressor of isolation. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Isoproterenol attenuates high vascular pressure-induced permeability increases in isolated rat lungs.

Science.gov (United States)

Parker, J C; Ivey, C L

1997-12-01

To separate the contributions of cellular and basement membrane components of the alveolar capillary barrier to the increased microvascular permeability induced by high pulmonary venous pressures (Ppv), we subjected isolated rat lungs to increases in Ppv, which increased capillary filtration coefficient (Kfc) without significant hemorrhage (31 cmH2O) and with obvious extravasation of red blood cells (43 cmH2O). Isoproterenol (20 microM) was infused in one group (Iso) to identify a reversible cellular component of injury, and residual blood volumes were measured to assess extravasation of red blood cells through ruptured basement membranes. In untreated lungs (High Ppv group), Kfc increased 6.2 +/- 1.3 and 38.3 +/- 15.2 times baseline during the 31 and 43 cmH2O Ppv states. In Iso lungs, Kfc was 36.2% (P Kfc increases at moderate Ppv, possibly because of an endothelial effect, but it did not affect red cell extravasation at higher vascular pressures.

Characterization of Staphylococcus aureus isolates from raw milk sources in Victoria, Australia.

Science.gov (United States)

McMillan, Kate; Moore, Sean C; McAuley, Catherine M; Fegan, Narelle; Fox, Edward M

2016-07-29

Highly pathogenic strains of Staphylococcus aureus can cause disease in both humans and animals. In animal species, including ruminants, S. aureus may cause severe or sub-clinical mastitis. Dairy animals with mastitis frequently shed S. aureus into the milk supply which can lead to food poisoning in humans. The aim of this study was to use genotypic and immunological methods to characterize S. aureus isolates from milk-related samples collected from 7 dairy farms across Victoria. A total of 30 S. aureus isolates were collected from milk and milk filter samples from 3 bovine, 3 caprine and 1 ovine dairy farms across Victoria, Australia. Pulsed Field Gel Electrophoresis (PFGE) identified 11 distinct pulsotypes among isolates; all caprine and ovine isolates shared greater than 80 % similarity regardless of source. Conversely, bovine isolates showed higher diversity. Multi-Locus Sequence Typing (MLST) identified 5 different sequence types (STs) among bovine isolates, associated with human or ruminant lineages. All caprine and ovine isolates were ST133, or a single allele variant of ST133. Two new novel STs were identified among isolates in this study (ST3183 and ST3184). With the exception of these 2 new STs, eBURST analysis predicted all other STs to be founding members of their associated clonal complexes (CCs). Analysis of genetic markers revealed a diverse range of classical staphylococcal enterotoxins (SE) among isolates, with 11 different SEs identified among bovine isolates, compared with just 2 among caprine and ovine isolates. None of the isolates contained mecA, or were resistant to oxacillin. The only antibiotic resistance identified was that of a single isolate resistant to penicillin; this isolate also contained the penicillin resistance gene blaZ. Production of SE was observed at 16 °C and/or 37 °C in milk, however no SE production was detected at 12 °C. Although this study characterized a limited number of isolates, bovine-associated isolates

Diversity of Papaya ringspot virus isolates in Puerto Rico

Science.gov (United States)

Papaya ringspot virus (PRSV) devastates papaya production worldwide. In Puerto Rico, papaya fields can be completely infected with PRSV within a year of planting. Information about the diversity of the Puerto Rican PRSV population is relevant in order to establish a control strategy in the island. T...

Use of Comparative Genomics To Characterize the Diversity of Acinetobacter baumannii Surveillance Isolates in a Health Care Institution

Science.gov (United States)

Wallace, Lalena; Daugherty, Sean C.; Nagaraj, Sushma; Johnson, J. Kristie; Harris, Anthony D.

2016-01-01

Despite the increasing prevalence of the nosocomial pathogen Acinetobacter baumannii, little is known about which genomic components contribute to clinical presentation of this important pathogen. Most whole-genome comparisons of A. baumannii have focused on specific genomic regions associated with phenotypes in a limited number of genomes. In this work, we describe the results of a whole-genome comparative analysis of 254 surveillance isolates of Acinetobacter species, 203 of which were A. baumannii, isolated from perianal swabs and sputum samples collected as part of an infection control active surveillance program at the University of Maryland Medical Center. The collection of surveillance isolates includes both carbapenem-susceptible and -resistant isolates. Based on the whole-genome phylogeny, the A. baumannii isolates collected belong to two major phylogenomic lineages. Results from multilocus sequence typing indicated that one of the major phylogenetic groups of A. baumannii was comprised solely of strains from the international clonal lineage 2. The genomic content of the A. baumannii isolates was examined using large-scale BLAST score ratio analysis to identify genes that are associated with carbapenem-susceptible and -resistant isolates, as well as genes potentially associated with the source of isolation. This analysis revealed a number of genes that were exclusive or at greater frequency in each of these classifications. This study is the most comprehensive genomic comparison of Acinetobacter isolates from a surveillance study to date and provides important information that will contribute to our understanding of the success of A. baumannii as a human pathogen. PMID:27458211

Spatial prisoner's dilemma games with increasing neighborhood size and individual diversity on two interdependent lattices

Energy Technology Data Exchange (ETDEWEB)

Meng, Xiao-Kun [Tianjin Key Laboratory of Intelligence Computing and Novel Software Technology, Tianjin University of Technology, Tianjin 300384 (China); Key Laboratory of Computer Vision and System (Ministry of Education), Tianjin University of Technology, Tianjin 300384 (China); Xia, Cheng-Yi, E-mail: xialooking@163.com [Tianjin Key Laboratory of Intelligence Computing and Novel Software Technology, Tianjin University of Technology, Tianjin 300384 (China); Key Laboratory of Computer Vision and System (Ministry of Education), Tianjin University of Technology, Tianjin 300384 (China); Gao, Zhong-Ke [School of Electrical Engineering and Automation, Tianjin University, Tianjin 300072 (China); Wang, Li; Sun, Shi-Wen [Tianjin Key Laboratory of Intelligence Computing and Novel Software Technology, Tianjin University of Technology, Tianjin 300384 (China); Key Laboratory of Computer Vision and System (Ministry of Education), Tianjin University of Technology, Tianjin 300384 (China)

2015-04-03

Highlights: • A novel PDG model with individual diversity and utility interdependency is proposed. • Diversity can be represented by players with different strategy spreading abilities. • Interdependency is implemented by the payoff correlation between two lattices. • Cooperation can be remarkably promoted by combining these two kinds of mechanisms. - Abstract: We present an improved spatial prisoner's dilemma game model which simultaneously considers the individual diversity and increasing neighborhood size on two interdependent lattices. By dividing the players into influential and non-influential ones, we can discuss the impact of individual diversity on the cooperative behaviors. Meanwhile, we implement the utility interdependency by integrating the payoff correlations between two lattices. Extensive simulations indicate that the optimal density of influential players exists for the cooperation to be promoted, and can be further facilitated through the utility coupling. Current results are beneficial to understanding the origin of cooperation among selfish agents among realistic scenarios.

Spatial prisoner's dilemma games with increasing neighborhood size and individual diversity on two interdependent lattices

International Nuclear Information System (INIS)

Meng, Xiao-Kun; Xia, Cheng-Yi; Gao, Zhong-Ke; Wang, Li; Sun, Shi-Wen

2015-01-01

Highlights: • A novel PDG model with individual diversity and utility interdependency is proposed. • Diversity can be represented by players with different strategy spreading abilities. • Interdependency is implemented by the payoff correlation between two lattices. • Cooperation can be remarkably promoted by combining these two kinds of mechanisms. - Abstract: We present an improved spatial prisoner's dilemma game model which simultaneously considers the individual diversity and increasing neighborhood size on two interdependent lattices. By dividing the players into influential and non-influential ones, we can discuss the impact of individual diversity on the cooperative behaviors. Meanwhile, we implement the utility interdependency by integrating the payoff correlations between two lattices. Extensive simulations indicate that the optimal density of influential players exists for the cooperation to be promoted, and can be further facilitated through the utility coupling. Current results are beneficial to understanding the origin of cooperation among selfish agents among realistic scenarios

Biochar amendment decreases soil microbial biomass and increases bacterial diversity in Moso bamboo (Phyllostachys edulis) plantations under simulated nitrogen deposition

Science.gov (United States)

Li, Quan; Lei, Zhaofeng; Song, Xinzhang; Zhang, Zhiting; Ying, Yeqing; Peng, Changhui

2018-04-01

Biochar amendment has been proposed as a strategy to improve acidic soils after overuse of nitrogen fertilizers. However, little is known of the role of biochar in soil microbial biomass carbon (MBC) and bacterial community structure and diversity after soil acidification induced by nitrogen (N) deposition. Using high-throughput sequencing of the 16S rRNA gene, we determined the effects of biochar amendment (BC0, 0 t bamboo biochar ha‑1 BC20, 20 t bamboo biochar ha‑1 and BC40, 40 t bamboo biochar ha‑1) on the soil bacterial community structure and diversity in Moso bamboo plantations that had received simulated N deposition (N30, 30 kg N ha‑1 yr‑1 N60, 60 kg N ha‑1 yr‑1 N90, 90 kg N ha‑1 yr‑1 and N-free) for 21 months. After treatment of N-free plots, BC20 significantly increased soil MBC and bacterial diversity, while BC40 significantly decreased soil MBC but increased bacterial diversity. When used to amend N30 and N60 plots, biochar significantly decreased soil MBC and the reducing effect increased with biochar amendment amount. However, these significant effects were not observed in N90 plots. Under N deposition, biochar amendment largely increased soil bacterial diversity, and these effects depended on the rates of N deposition and biochar amendment. Soil bacterial diversity was significantly related to the soil C/N ratio, pH, and soil organic carbon content. These findings suggest an optimal approach for using biochar to offset the effects of N deposition in plantation soils and provide a new perspective for understanding the potential role of biochar amendments in plantation soil.

Coral-Associated Actinobacteria: Diversity, Abundance, and Biotechnological Potentials

Science.gov (United States)

Mahmoud, Huda M.; Kalendar, Aisha A.

2016-01-01

Marine Actinobacteria, particularly coral-associated Actinobacteria, have attracted attention recently. In this study, the abundance and diversity of Actinobacteria associated with three types of coral thriving in a thermally stressed coral reef system north of the Arabian Gulf were investigated. Coscinaraea columna, Platygyra daedalea and Porites harrisoni have been found to harbor equivalent numbers of culturable Actinobacteria in their tissues but not in their mucus. However, different culturable actinobacterial communities have been found to be associated with different coral hosts. Differences in the abundance and diversity of Actinobacteria were detected between the mucus and tissue of the same coral host. In addition, temporal and spatial variations in the abundance and diversity of the cultivable actinobacterial communities were detected. In total, 19 different actinobacterial genera, namely Micrococcus, Brachybacterium, Brevibacterium, Streptomyces, Micromonospora, Renibacterium, Nocardia, Microbacterium, Dietzia, Cellulomonas, Ornithinimicrobium, Rhodococcus, Agrococcus, Kineococcus, Dermacoccus, Devriesea, Kocuria, Marmoricola, and Arthrobacter, were isolated from the coral tissue and mucus samples. Furthermore, 82 isolates related to Micromonospora, Brachybacterium, Nocardia, Micrococcus, Arthrobacter, Rhodococcus, and Streptomyces showed antimicrobial activities against representative Gram-positive and/or Gram-negative bacteria. Even though Brevibacterium and Kocuria were the most dominant actinobacterial isolates, they failed to show any antimicrobial activity, whereas less dominant genera, such as Streptomyces, did show antimicrobial activity. Focusing on the diversity of coral-associated Actinobacteria may help to understand how corals thrive under harsh environmental conditions and may lead to the discovery of novel antimicrobial metabolites with potential biotechnological applications. PMID:26973601

Genome Structural Diversity among 31 Bordetella pertussis Isolates from Two Recent U.S. Whooping Cough Statewide Epidemics.

Science.gov (United States)

Bowden, Katherine E; Weigand, Michael R; Peng, Yanhui; Cassiday, Pamela K; Sammons, Scott; Knipe, Kristen; Rowe, Lori A; Loparev, Vladimir; Sheth, Mili; Weening, Keeley; Tondella, M Lucia; Williams, Margaret M

2016-01-01

During 2010 and 2012, California and Vermont, respectively, experienced statewide epidemics of pertussis with differences seen in the demographic affected, case clinical presentation, and molecular epidemiology of the circulating strains. To overcome limitations of the current molecular typing methods for pertussis, we utilized whole-genome sequencing to gain a broader understanding of how current circulating strains are causing large epidemics. Through the use of combined next-generation sequencing technologies, this study compared de novo, single-contig genome assemblies from 31 out of 33 Bordetella pertussis isolates collected during two separate pertussis statewide epidemics and 2 resequenced vaccine strains. Final genome architecture assemblies were verified with whole-genome optical mapping. Sixteen distinct genome rearrangement profiles were observed in epidemic isolate genomes, all of which were distinct from the genome structures of the two resequenced vaccine strains. These rearrangements appear to be mediated by repetitive sequence elements, such as high-copy-number mobile genetic elements and rRNA operons. Additionally, novel and previously identified single nucleotide polymorphisms were detected in 10 virulence-related genes in the epidemic isolates. Whole-genome variation analysis identified state-specific variants, and coding regions bearing nonsynonymous mutations were classified into functional annotated orthologous groups. Comprehensive studies on whole genomes are needed to understand the resurgence of pertussis and develop novel tools to better characterize the molecular epidemiology of evolving B. pertussis populations. IMPORTANCE Pertussis, or whooping cough, is the most poorly controlled vaccine-preventable bacterial disease in the United States, which has experienced a resurgence for more than a decade. Once viewed as a monomorphic pathogen, B. pertussis strains circulating during epidemics exhibit diversity visible on a genome structural

Investigating genetic diversity and habitat dynamics in Plantago brutia (Plantaginaceae), implications for the management of narrow endemics in Mediterranean mountain pastures.

Science.gov (United States)

De Vita, A; Bernardo, L; Gargano, D; Palermo, A M; Peruzzi, L; Musacchio, A

2009-11-01

Many factors have contributed to the richness of narrow endemics in the Mediterranean, including long-lasting human impact on pristine landscapes. The abandonment of traditional land-use practices is causing forest recovery throughout the Mediterranean mountains, by increasing reduction and fragmentation of open habitats. We investigated the population genetic structure and habitat dynamics of Plantago brutia Ten., a narrow endemic in mountain pastures of S Italy. Some plants were cultivated in the botanical garden to explore the species' breeding system. Genetic diversity was evaluated based on inter-simple sequence repeat (ISSR) polymorphisms in 150 individuals from most of known stands. Recent dynamics in the species habitat were checked over a 14-year period. Flower phenology, stigma receptivity and experimental pollinations revealed protogyny and self-incompatibility. With the exception of very small and isolated populations, high genetic diversity was found at the species and population level. amova revealed weak differentiation among populations, and the Mantel test suggested absence of isolation-by-distance. Multivariate analysis of population and genetic data distinguished the populations based on genetic richness, size and isolation. Landscape analyses confirmed recent reduction and isolation of potentially suitable habitats. Low selfing, recent isolation and probable seed exchange may have preserved P. brutia populations from higher loss of genetic diversity. Nonetheless, data related to very small populations suggest that this species may suffer further fragmentation and isolation. To preserve most of the species' genetic richness, future management efforts should consider the large and isolated populations recognised in our analyses.

RNA-Seq analysis of isolate- and growth phase-specific differences in the global transcriptomes of enteropathogenic Escherichia coli prototype isolates

Science.gov (United States)

Hazen, Tracy H.; Daugherty, Sean C.; Shetty, Amol; Mahurkar, Anup A.; White, Owen; Kaper, James B.; Rasko, David A.

2015-01-01

Enteropathogenic Escherichia coli (EPEC) are a leading cause of diarrheal illness among infants in developing countries. E. coli isolates classified as typical EPEC are identified by the presence of the locus of enterocyte effacement (LEE) and the bundle-forming pilus (BFP), and absence of the Shiga-toxin genes, while the atypical EPEC also encode LEE but do not encode BFP or Shiga-toxin. Comparative genomic analyses have demonstrated that EPEC isolates belong to diverse evolutionary lineages and possess lineage- and isolate-specific genomic content. To investigate whether this genomic diversity results in significant differences in global gene expression, we used an RNA sequencing (RNA-Seq) approach to characterize the global transcriptomes of the prototype typical EPEC isolates E2348/69, B171, C581-05, and the prototype atypical EPEC isolate E110019. The global transcriptomes were characterized during laboratory growth in two different media and three different growth phases, as well as during adherence of the EPEC isolates to human cells using in vitro tissue culture assays. Comparison of the global transcriptomes during these conditions was used to identify isolate- and growth phase-specific differences in EPEC gene expression. These analyses resulted in the identification of genes that encode proteins involved in survival and metabolism that were coordinately expressed with virulence factors. These findings demonstrate there are isolate- and growth phase-specific differences in the global transcriptomes of EPEC prototype isolates, and highlight the utility of comparative transcriptomics for identifying additional factors that are directly or indirectly involved in EPEC pathogenesis. PMID:26124752

[Isolation and physiological characteristics of endophytic actinobacteria from medicinal plants].

Science.gov (United States)

Du, Huijing; Su, Jing; Yu, Liyan; Zhang, Yuqin

2013-01-04

To isolate, incubate and characterize cultivable endophytic antinobacteria from medicinal plants, and analyze the diversity of the endophytic antinobacteria, then explore the novel microbial resources. Ten media were used to isolate endophytic antinobacteria from 37 fresh medicinal plant tissue samples. The optimal cultivation conditions for endophytic antinobacteria were determined by comparison. Based on the morphology of the colonies and cells of the new isolates, we chose 174 isolates to analyze their 16S rRNA gene sequences and the diversity of the medicinal plant endophytic antinobacteria. The physiological characteristics of 27 representative strains were studied using Biolog GEN III MicroPlates, API 50CH and API ZYM kits. In total 940 endophytics affiliated to 47 genera of 30 families were isolated, among which more than 600 actinobacteria belonged to 34 genera and 7 unknown taxa. Good growth of the endophytic antinobacteria on PYG (peptone-yeast-glycerol) medium with pH 7.2 at 28-32 degrees C was observed. Physiological characteristics differences of these isolates related to their phylogenetic relationships. Greater differences were shown among the strains from the same host plants than those from differ,ent plants grown in the same area. There are great diverse endophytic actinobacteria inside the medicinal plants. No direct relationship of the endophytic actinobacteria from medicinal plants with the host plants in the sole carbon source utilization, fermentation of carbon sources to produce acid and the enzyme activities was found, while it seemed that the physiological characteristics of the isolates related to the geographical distribution of their host.

Unraveling the genetic diversity and phylogeny of Leishmania RNA virus 1 strains of infected Leishmania isolates circulating in French Guiana.

Science.gov (United States)

Tirera, Sourakhata; Ginouves, Marine; Donato, Damien; Caballero, Ignacio S; Bouchier, Christiane; Lavergne, Anne; Bourreau, Eliane; Mosnier, Emilie; Vantilcke, Vincent; Couppié, Pierre; Prevot, Ghislaine; Lacoste, Vincent

2017-07-01

Leishmania RNA virus type 1 (LRV1) is an endosymbiont of some Leishmania (Vianna) species in South America. Presence of LRV1 in parasites exacerbates disease severity in animal models and humans, related to a disproportioned innate immune response, and is correlated with drug treatment failures in humans. Although the virus was identified decades ago, its genomic diversity has been overlooked until now. We subjected LRV1 strains from 19 L. (V.) guyanensis and one L. (V.) braziliensis isolates obtained from cutaneous leishmaniasis samples identified throughout French Guiana with next-generation sequencing and de novo sequence assembly. We generated and analyzed 24 unique LRV1 sequences over their full-length coding regions. Multiple alignment of these new sequences revealed variability (0.5%-23.5%) across the entire sequence except for highly conserved motifs within the 5' untranslated region. Phylogenetic analyses showed that viral genomes of L. (V.) guyanensis grouped into five distinct clusters. They further showed a species-dependent clustering between viral genomes of L. (V.) guyanensis and L. (V.) braziliensis, confirming a long-term co-evolutionary history. Noteworthy, we identified cases of multiple LRV1 infections in three of the 20 Leishmania isolates. Here, we present the first-ever estimate of LRV1 genomic diversity that exists in Leishmania (V.) guyanensis parasites. Genetic characterization and phylogenetic analyses of these viruses has shed light on their evolutionary relationships. To our knowledge, this study is also the first to report cases of multiple LRV1 infections in some parasites. Finally, this work has made it possible to develop molecular tools for adequate identification and genotyping of LRV1 strains for diagnostic purposes. Given the suspected worsening role of LRV1 infection in the pathogenesis of human leishmaniasis, these data have a major impact from a clinical viewpoint and for the management of Leishmania-infected patients.

Enhancing the Careers of Under-Represented Junior Faculty in Biomedical Research: The Summer Institute Program to Increase Diversity (SIPID).

Science.gov (United States)

Rice, Treva K; Liu, Li; Jeffe, Donna B; Jobe, Jared B; Boutjdir, Mohamed; Pace, Betty S; Rao, Dabeeru C

2014-01-01

The Summer Institute Program to Increase Diversity (SIPID) in Health-Related Research is a career advancement opportunity sponsored by the National Heart, Lung, and Blood Institute. Three mentored programs address difficulties experienced by junior investigators in establishing independent research careers and academic advancement. Aims are to increase the number of faculty from under-represented minority groups who successfully compete for external research funding. Data were collected using a centralized data-entry system from three Summer Institutes. Outcomes include mentees' satisfaction rating about the program, grant and publications productivity and specific comments. Fifty-eight junior faculty mentees (38% male) noticeably improved their rates of preparing/submitting grant applications and publications, with a 18-23% increase in confidence levels in planning and conducting research. According to survey comments, the training received in grantsmanship skills and one-on-one mentoring were the most valuable program components. The SIPID mentoring program was highly valued by the junior faculty mentees. The program will continue in 2011-2014 as PRIDE (PRogram to Increase Diversity among individuals Engaged in health-related research). Long-term follow-up of current mentees will be indexed at five years post training (2013). In summary, these mentoring programs hope to continue increasing the diversity of the next generation of scientists in biomedical research.

Genetic diversity of Escherichia coli isolated from commercial swine ...

African Journals Online (AJOL)

Administrator

2011-09-07

Sep 7, 2011 ... The objective of this study was to use enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) ... Furthermore, the genotypes and phylogenetic relationship of all isolates ... bacterial taxonomy proves problematic when .... The cell pellet was resuspended in 567 µl TE and mixed with 30. 10% SDS ...

Parasympathetic denervation increases responses to VIP in isolated rat parotid acini

International Nuclear Information System (INIS)

McMillian, M.K.; Talamo, B.R.

1989-01-01

Vasoactive intestinal peptide (VIP) is a putative neurotransmitter found in the salivary glands of many species, including the rat parotid gland. Parasympathetic denervation has been reported to deplete VIP in the rat parotid gland and to lead to supersensitivity to this peptide in vivo. We have compared the effects of VIP on acini isolated from parasympathetically denervated and unoperated parotid glands to examine possible supersensitivity to the peptide in vitro. VIP normally produced responses similar to those obtained with a low concentration of the beta adrenergic agonist isoproterenol (ISO), but strikingly different from the effects obtained with the muscarinic agonist carbachol (CARB). In parotid membrane preparations, VIP stimulated adenylate cyclase activity. Dissociated acini treated with VIP showed increases in cAMP accumulation and amylase release which were potentiated by forskolin and also by inhibition of phosphodiesterase. After parasympathetic denervation, maximal effects of VIP on adenylate cyclase, cAMP accumulation and amylase release in intact cells were increased two- to five-fold over contralateral control (or unoperated) parotid responses. The increase in adenylate cyclase-mediated responses after denervation was specific to VIP; there was no increased response nor increased sensitivity of any of these responses to ISO. Specific [125I]VIP binding to parotid acini increased two-fold per gland and three-fold per mg of protein after denervation; this probably explains the observed increases in the response to VIP