scholarly journals Dynamics of QoI Sensitivity in Mycosphaerella fijiensis in Costa Rica During 2000 to 2003

2007 ◽  
Vol 97 (11) ◽  
pp. 1451-1457 ◽  
Author(s):  
A. F. Amil ◽  
S. P. Heaney ◽  
C. Stanger ◽  
M. W. Shaw
Keyword(s):  
Costa Rica ◽  
Large Scale ◽  
Spatial Scales ◽  
Quantitative Polymerase Chain Reaction ◽  
Single Point ◽  
Oxidase Inhibitor ◽  
Amplification Refractory Mutation System ◽  
Single Point Mutation ◽  
Mycosphaerella Fijiensis ◽  
Black Sigatoka

From 1997 onward, the strobilurin fungicide azoxystrobin was widely used in the main banana-production zone in Costa Rica against Mycosphaerella fijiensis var. difformis causing black Sigatoka of banana. By 2000, isolates of M. fijiensis with resistance to the quinolene oxidase inhibitor fungicides were common on some farms in the area. The cause was a single point mutation from glycine to alanine in the fungal target protein, cytochrome b gene. An amplification refractory mutation system Scorpion quantitative polymerase chain reaction assay was developed and used to determine the frequency of G143A allele in samples of M. fijiensis. Two hierarchical surveys of spatial variability, in 2001 and 2002, found no significant variation in frequency on spatial scales <10 m. This allowed the frequency of G143A alleles on a farm to be estimated efficiently by averaging single samples taken at two fixed locations. The frequency of G143A allele in bulk samples from 11 farms throughout Costa Rica was determined at 2-month intervals. There was no direct relationship between the number of spray applications and the frequency of G143A on individual farms. Instead, the frequency converged toward regional averages, presumably due to the large-scale mixing of ascospores dispersed by wind. Using trap plants in an area remote from the main producing area, immigration of resistant ascospores was detected as far as 6 km away both with and against the prevailing wind.

Multilevel Evolution: The Fate of Duplicated Genes

2002 ◽  
Vol 216 (1) ◽  
Author(s):  
Paulien Hogeweg
Keyword(s):  
Information Integration ◽  
Large Scale ◽  
Evolutionary Dynamics ◽  
Single Point ◽  
Gene Content ◽  
Minor Role ◽  
Single Point Mutation ◽  
Duplicated Genes ◽  
A Genome ◽  
Multilevel Evolution

Biological evolution is a multilevel process and should be studied as such. A first, important step in studying evolution in this way has been the work of Peter Schuster and co-workers on RNA evolution. For RNA the genotype-phenotype mapping can be calculated explicitly. The resulting evolutionary dynamics is dominated by neutral paths, and the potential of major change by a single point mutation.Examining whole genomes, of which about 60 are now available, we see that gene content of genomes is changing relatively rapidly: gene duplication, gene loss and gene generation is ubiquitous. In fact, it seems that point-mutations play a relatively minor role, relative to changes in gene regulation and gene content in adaptive evolution.Large scale micro-array studies, in which the expression of every gene can be measured simultaneously, give a first glimpse of the `division of labor´ between duplicated genes. A preliminary analysis suggests that differential expression is often the primary event which allows duplicated genes to be maintained in a genome, but alternate routes also exist, most notably on the one hand the mere need of a lot of product, and on the other hand differentiation within multi-protein complexes consisting of homologous genes.I will discuss these results in terms of multilevel evolution. in particular in terms of information integration and the alternatives of `individual based´

scholarly journals Monitoring of Pyrethroid Resistance Allele Frequency in the Common Bed Bug (Cimex lectularius) in the Republic of Korea

2020 ◽  
Vol 58 (1) ◽  
pp. 99-102
Author(s):  
Susie Cho ◽  
Heung-Chul Kim ◽  
Sung-Tae Chong ◽  
Terry A. Klein ◽  
Deok Ho Kwon ◽  
...  
Keyword(s):  
Large Scale ◽  
Pyrethroid Resistance ◽  
Single Point ◽  
Point Mutations ◽  
Monitoring Program ◽  
Cimex Lectularius ◽  
Single Point Mutation ◽  
Resistance Allele ◽  
Bed Bugs ◽  
Bed Bug

Two-point mutations (V419L and L925I) on the voltage-sensitive sodium channel of bed bugs (<i>Cimex lectularius</i>) are known to confer pyrethroid resistance. To determine the status of pyrethroid resistance in bed bugs in Korea, resistance allele frequencies of bed bug strains collected from several US military installations in Korea and Mokpo, Jeollanamdo, from 2009-2019 were monitored using a quantitative sequencing. Most bed bugs were determined to have both of the point mutations except a few specimens, collected in 2009, 2012 and 2014, having only a single point mutation (L925I). No susceptible allele was observed in any of the bed bugs examined, suggesting that pyrethroid resistance in bed bug populations in Korea has reached a serious level. Large scale monitoring is required to increase our knowledge on the distribution and prevalence of pyrethroid resistance in bed bug populations in Korea. Based on present study, it is urgent to restrict the use of pyrethroids and to introduce effective alternative insecticides. A nation-wide monitoring program to determine the pyrethroid resistance level in bed bugs and to select alternative insecticides should be implemented.

Simple and Reliable Factor V Genotyping by PNA-Mediated PCR Clamping

1998 ◽  
Vol 79 (04) ◽  
pp. 773-777 ◽  
Author(s):  
Moira Behn ◽  
Marcus Schuermann
Keyword(s):  
Venous Thrombosis ◽  
Large Scale ◽  
Single Point ◽  
Activated Protein C ◽  
Factor V Leiden ◽  
Single Point Mutation ◽  
Factor V ◽  
Apc Resistance ◽  
Novel Approach ◽  
Pcr Rflp

SummaryResistance to activated protein C (APC resistance) is the most common cause of thrombophilia and linked to a single point mutation in the factor V gene (G>A transition at nucleotide 1691). In the past, several PCR based methods have been proposed to determine the allelostatus of individual patients from small amounts of blood DNA including PCR followed by restriction fragment length polymorphism detection (PCR-RFLP), PCR using sequence-specific primers (PCR-SSP) and oligonucleotide ligation assay (OLA). Here, we present a novel approach based on the method of peptide nucleic acid(PNA)-mediated PCR clamping which is extremely sensitive to base pair mismatches. If PNAs specific for the two allelic variants are applied separately in each case a clear discrimination between a heterozygous or homozygous normal or homozygous Factor V Leiden status is possible and no further confirmation step is required. In a prospective study, 60 patients with suspected venous thrombosis events were tested and compared to the conventional PCR-RFLP technique. The concordance between both methods was 100%. PNA-based factor V genotyping, therefore, should be considered for large scale screening of those patients considered to be at risk for deep venous thrombosis.

Production of isomelezitose from sucrose by engineered glucansucrases

Amylase ◽  
2017 ◽  
Vol 1 (1) ◽  
Author(s):  
Gregory L. Côté ◽  
Christopher A. Dunlap ◽  
Karl E. Vermillion ◽  
Christopher D. Skory
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Biomedical Applications ◽  
Large Scale ◽  
Single Point ◽  
Single Point Mutation ◽  
Scale Production ◽  
Acceptor Substrate ◽  
Large Scale Production ◽  
High Yields

AbstractCertain lactic acid bacteria produce glycosyltransferases known as glucansucrases, which synthesize α-D-glucans via glucosyl transfer from sucrose. We recently reported on the formation of the unusual trisaccharide isomelezitose in low yields by a variety of glucansucrases. Isomelezitose is a rare non-reducing trisaccharide, with the structure α-d-glucopyranosyl- (1→6)-β-d-fructofuranosyl-(2↔1)-α-d-glucopyranoside. In this work, we describe the synthesis of isomelezitose in high yields by variants of glucansucrases engineered to contain a single point mutation at a key leucine residue involved in acceptor substrate binding. Some variants produce isomelezitose in yields up to 57%. This method is amenable to large-scale production of isomelezitose for food, industrial and biomedical applications.

scholarly journals CRISPR-Based Genetic Manipulation of Candida Species: Historical Perspectives and Current Approaches

2021 ◽  
Vol 2 ◽  
Author(s):  
Deeva Uthayakumar ◽  
Jehoshua Sharma ◽  
Lauren Wensing ◽  
Rebecca S. Shapiro
Keyword(s):  
Large Scale ◽  
Gene Editing ◽  
Genetic Manipulation ◽  
Single Point ◽  
Antifungal Drug ◽  
Sexual Cycle ◽  
Single Point Mutation ◽  
Functional Genomic ◽  
Historical Perspectives ◽  
Genomic Studies

The Candida genus encompasses a diverse group of ascomycete fungi that have captured the attention of the scientific community, due to both their role in pathogenesis and emerging applications in biotechnology; the development of gene editing tools such as CRISPR, to analyze fungal genetics and perform functional genomic studies in these organisms, is essential to fully understand and exploit this genus, to further advance antifungal drug discovery and industrial value. However, genetic manipulation of Candida species has been met with several distinctive barriers to progress, such as unconventional codon usage in some species, as well as the absence of a complete sexual cycle in its diploid members. Despite these challenges, the last few decades have witnessed an expansion of the Candida genetic toolbox, allowing for diverse genome editing applications that range from introducing a single point mutation to generating large-scale mutant libraries for functional genomic studies. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology is among the most recent of these advancements, bringing unparalleled versatility and precision to genetic manipulation of Candida species. Since its initial applications in Candida albicans, CRISPR-Cas9 platforms are rapidly evolving to permit efficient gene editing in other members of the genus. The technology has proven useful in elucidating the pathogenesis and host-pathogen interactions of medically relevant Candida species, and has led to novel insights on antifungal drug susceptibility and resistance, as well as innovative treatment strategies. CRISPR-Cas9 tools have also been exploited to uncover potential applications of Candida species in industrial contexts. This review is intended to provide a historical overview of genetic approaches used to study the Candida genus and to discuss the state of the art of CRISPR-based genetic manipulation of Candida species, highlighting its contributions to deciphering the biology of this genus, as well as providing perspectives for the future of Candida genetics.

scholarly journals Characterization of Benomyl Resistance in Mycosphaerella fijiensis, Cause of Black Sigatoka of Banana, in Costa Rica

Plant Disease ◽  
1998 ◽  
Vol 82 (8) ◽  
pp. 931-934 ◽  
Author(s):  
Ronald A. Romero ◽  
Turner B. Sutton
Keyword(s):  
Costa Rica ◽  
Disease Severity ◽  
Incubation Time ◽  
High Frequency ◽  
Lower Sensitivity ◽  
Mycosphaerella Fijiensis ◽  
Black Sigatoka ◽  
History Of ◽  
Banana Plantations

Sixty-eight and eighty-six percent of monoascosporic isolates of Mycosphaerella fijiensis from two banana plantations in Costa Rica, in which benomyl was used for ≈10 years to control black Sigatoka, were resistant to benomyl in February and November 1994, respectively. No resistance to benomyl was detected in isolates collected during February 1994 from farms with no history of benomyl use that were located ≈50 km from the nearest banana plantations. Only 1% of isolates was resistant to benomyl in a sample taken during November 1994. In three additional banana farms where benomyl had not been used for 3 to 5 years before sampling, ben-omyl resistance persisted at a high frequency. Benomyl-resistant and -sensitive isolates were distributed equally throughout the range of isolate sensitivity to propiconazole, indicating no relationship between resistance to benomyl and lower sensitivity to propiconazole but double resistance to these two compounds. Five benomyl-resistant and five benomyl-sensitive isolates of M. fijiensis were inoculated to banana plants under greenhouse conditions. Benomyl-resistant isolates were more aggressive than benomyl-sensitive isolates, as determined by measures of disease severity, incubation time, and number of lesions at 40 days after inoculation.

Computational multiscale studies of collagen tissues in the context of brittle bone disease osteogenesis imperfecta

2010 ◽  
Vol 1274 ◽  
Author(s):  
Simone Vesentini ◽  
Alfonso Gautieri ◽  
Alberto Redaelli ◽  
Markus J. Buehler
Keyword(s):  
Osteogenesis Imperfecta ◽  
Large Scale ◽  
Multiple Scales ◽  
Broad Class ◽  
Genetic Disorder ◽  
Single Point ◽  
Collagen Fibrils ◽  
Coarse Grained ◽  
Single Point Mutation ◽  
Length Scales

AbstractOsteogenesis imperfecta (abbreviated as OI) is a genetic disorder in collagen characterized by mechanically weakened tendon, fragile bones, skeletal deformities and in severe cases prenatal death. Even though many studies have attempted to associate specific mutation types with phenotypic severity, the molecular and mesoscale mechanisms by which a single point mutation influences the mechanical behavior of tissues at multiple length-scales remain unknown. Here we review results of a hierarchy of full atomistic and mesoscale simulations that demonstrated that OI mutations severely compromise the mechanical properties of collagenous tissues at multiple scales, from single molecules to collagen fibrils. Notably, mutations that lead to the most severe OI phenotype correlate with the strongest effects, leading to weakened intermolecular adhesion, increased intermolecular spacing, reduced stiffness, as well as a reduced failure strength of collagen fibrils (Gautieri et al., Biophys. J., 2009). Our study explains how single point mutations can control the breakdown of tissue at much larger length-scales, a question of great relevance for a broad class of genetic diseases. Furthermore, by extending the MARTINI coarse-grained force field, we provide a new modeling tool to study collagen molecules and fibrils at much larger scales than accessible to existing full atomistic models, while incorporating key chemical and mechanical features and thereby presents a powerful approach to computational materiomics (Gautieri et al., Journal of Chemical Theory and Computation, 2010). We describe the coarse-graining approach and present preliminary findings based on this model in applying it to large-scale models of molecular assemblies into fibrils.

scholarly journals Reaction of Four Musa Genotypes at Three Temperatures to Isolates of Mycosphaerella fijiensis from Different Geographical Regions

Plant Disease ◽  
1997 ◽  
Vol 81 (10) ◽  
pp. 1139-1142 ◽  
Author(s):  
Ronald A. Romero ◽  
Turner B. Sutton
Keyword(s):  
Costa Rica ◽  
Incubation Period ◽  
Disease Severity ◽  
Geographical Origin ◽  
Mycosphaerella Fijiensis ◽  
Black Sigatoka ◽  
Naturally Occurring ◽  
Geographical Regions ◽  
Incubation Periods ◽  
Growth Chambers

Two tetraploid banana hybrids, FHIA1 and FHIA2, with resistance to black Sigatoka, and two highly susceptible, naturally occurring triploids, Grand Naine and False Horn, were evaluated at three temperatures for their resistance to isolates of Mycosphaerella fijiensis from five geographical regions. The youngest open leaf of young plants was inoculated, and plants were incubated at 22, 26, and 30°C in growth chambers. Duration of the incubation period and disease severity were used to evaluate the reactions of the genotypes. The incubation period was the shortest at 26°C. Disease severity was greatest at 26°C on Grand Naine and False Horn, but there was no clear temperature effect for the FHIA genotypes. The incubation period was longer on both FHIA genotypes than on Grand Naine and False Horn. With few exceptions, isolates with the shortest incubation periods caused greater disease severity than those with longer incubation periods. The level of resistance between the two FHIA genotypes was similar, and both expressed high resistance across temperatures and isolates of M. fijiensis, indicating that no physiological races of the pathogen were detected. There were differences in durations of the incubation periods and disease severities associated with the geographical origin of the isolates. Isolates that originated in Honduras, Colombia, and Costa Rica produced more disease on Grand Naine and False Horn than did isolates from Cameroon and Asia. However, no differences associated with the geographical origin of the isolates were observed for both FHIA genotypes. Also, there were no differences in disease severities within isolates that originated from Honduras, Colombia, and Costa Rica.

scholarly journals VALIDATION OF SMOS L2 AND L3 SOIL MOISTURE PRODUCTS OVER THE DUERO BASIN AT DIFFERENT SPATIAL SCALES

2015 ◽  
Vol XL-7/W3 ◽  
pp. 1183-1188 ◽  
Author(s):  
A. González-Zamora ◽  
N. Sánchez ◽  
A. Gumuzzio ◽  
M. Piles ◽  
E. Olmedo ◽  
...  
Keyword(s):  
Soil Moisture ◽  
Large Scale ◽  
Spatial Scales ◽  
Single Point ◽  
Small Scale ◽  
Moisture Measurement ◽  
Duero Basin ◽  
Temporal Validation ◽  
Soil Moisture Measurement

An increasing number of permanent soil moisture measurement networks are nowadays providing the means for validating new remotely sensed soil moisture estimates such as those provided by the ESA’s Soil Moisture and Ocean Salinity (SMOS) mission. Two types of in situ measurement networks can be found: small-scale (100&ndash;10000 km<sup>2</sup>), which provide multiple ground measurements within a single satellite footprint, and large-scale (>10000 km<sup>2</sup>), which contain a single point observation per satellite footprint. This work presents the results of a comprehensive spatial and temporal validation of a long-term (January, 2010 to June, 2014) dataset of SMOS-derived soil moisture estimates using two in situ networks within the Duero basin (Spain). The first one is the Soil Moisture Measurement Stations Network of the University of Salamanca (REMEDHUS), which has been extensively applied for validation of soil moisture remote sensing observations, including SMOS. REMEDHUS can be considered within the small-scale network group (1300 km<sup>2</sup>). The other network started from an existing meteorological network from the Castilla y León region, where soil moisture probes were incorporated in 2012. This network can be considered within the large-scale group (65000 km<sup>2</sup>). Results from comparison to in situ show that the new reprocessed L2 product (v5.51) improves the accuracy of former soil moisture retrievals, making them suitable for developing new L3 products. Validation based on comparisons between dense/sparse networks showed that temporal patterns on soil moisture are well reproduced, whereas spatial patterns are difficult to depict given the different spatial representativeness of ground and satellite observations.

scholarly journals A tailored LNA clamping design principle: efficient, economized, specific and ultrasensitive for the detection of point mutations

2021 ◽  
Author(s):  
Hao Yang ◽  
Mengqiu Yan ◽  
Gaolian Xu ◽  
Xiaohua Qian ◽  
Ruiying Zhao ◽  
...  
Keyword(s):  
Gene Amplification ◽  
Design Principle ◽  
Single Point ◽  
Point Mutations ◽  
High Specificity ◽  
Locked Nucleic Acid ◽  
Amplification Refractory Mutation System ◽  
Single Point Mutation ◽  
Design Guideline ◽  
Specificity And Sensitivity

In the development of personalized medicine, the ultrasensitive detection of point mutations that correlate with diseases is important to improve the efficacy of treatment and guide clinical medication. In this study, locked nucleic acid (LNA) was introduced as an amplification suppressor of a massive number of wild-type alleles in an amplification refractory mutation system (ARMS) to achieve the detection of low-abundance mutations with high specificity and sensitivity of at least 0.1%. By integrating the length of clamp, base type, number and position of LNA modifications, we have established a “shortest length with the fewest LNA bases” principle from which each LNA base would play a key role in the affinity and the ability of single base discrimination could be improve. Finally, based on this LNA design guideline, a series of the most important single point mutation sites of epidermal growth factor receptor (EGFR) was verified to achieve the optimal amplification state which as low as 0.1% mutation gene amplification was not affected under the wild gene amplification was completely inhibited, demonstrating that the proposed design principle has good applicability and versatility and is of great significance for the detection of circulating tumor DNA.

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