Intraspecific variability of the acetolactate synthase gene

Weed Science ◽  
2004 ◽  
Vol 52 (2) ◽  
pp. 236-241 ◽  
Author(s):  
Patrick J. Tranel ◽  
Weilu Jiang ◽  
William L. Patzoldt ◽  
Terry R. Wright
Keyword(s):  
Sequence Data ◽  
Intraspecific Variability ◽  
Acetolactate Synthase ◽  
Nucleotide Polymorphisms ◽  
Gene Encoding ◽  
Resistance Development ◽  
Common Ragweed ◽  
The Common ◽  
Smooth Pigweed ◽  
Different Levels

Common ragweed and common cocklebur plants were collected at two sites each in Illinois, Minnesota, and Ohio to analyze intraspecific variability of the gene encoding acetolactate synthase (ALS). A 385-nucleotide fragment within the coding sequence ofALSwas compared among 24 plants of each of these two species from the six locations. Common ragweedALSwas highly variable, with polymorphisms observed at 48 (12.5%) of the 385 nucleotides among the 24 plants. Despite the numerous nucleotide polymorphisms, only two inferred amino acid polymorphisms were identified. No apparent population structure was suggested by theALSsequence data, indicating widespread gene flow consistent with the wind-pollinated nature of common ragweed. In contrast to common ragweed, noALSpolymorphisms were identified among the common cocklebur plants used in this study. As a basis for comparing the extremes observed between common ragweed and common cocklebur,ALSintraspecific variability also was investigated in 10 plants each of tall waterhemp and smooth pigweed. Normalized to the number of plants analyzed, the number of nucleotide polymorphisms for both tall waterhemp and smooth pigweed was greater than that in common cocklebur but less than that observed in common ragweed. Information on variability of herbicide target-site genes may be useful in predicting the likelihood for herbicide-resistance development. However, all four of the species investigated in this study have evolved resistance to ALS-inhibiting herbicides, despite the different levels ofALSvariability observed.

Characterization of a Common Ragweed (Ambrosia artemisiifolia) Population Resistant to ALS- and PPO-Inhibiting Herbicides

Weed Science ◽  
2012 ◽  
Vol 60 (3) ◽  
pp. 335-344 ◽  
Author(s):  
Stephanie L. Rousonelos ◽  
Ryan M. Lee ◽  
Murilo S. Moreira ◽  
Mark J. VanGessel ◽  
Patrick J. Tranel
Keyword(s):  
Dose Response ◽  
Sequence Data ◽  
Resistance Mechanism ◽  
Nuclear Gene ◽  
Acetolactate Synthase ◽  
Ambrosia Artemisiifolia ◽  
Common Ragweed ◽  
Dna Sequence Data ◽  
Molecular Marker Analysis ◽  
Dose Response Study

A population of common ragweed from Delaware was not controlled in the field by herbicides that inhibit acetolactate synthase (ALS) or protoporphyrinogen oxidase (PPO). Research was conducted to ascertain if this population was resistant to these herbicidal modes of action and, if so, to determine the resistance mechanism(s). Resistance was confirmed by dose-response studies on greenhouse-grown plants with multiple ALS- and PPO-inhibiting herbicides. DNA sequence data revealed that resistance to ALS-inhibiting herbicides was due to the previously reported W574L ALS mutation. To assist in determining the mechanism of resistance to PPO-inhibiting herbicides, an F2population was derived from a cross between the resistant biotype (Del-R) and a sensitive biotype (DV1-S). This population segregated in the ratio of three resistant : one sensitive when treated with fomesafen, indicating that resistance to PPO-inhibiting herbicides was conferred by a single, (incompletely) dominant, nuclear gene. Sequences of the target-site genes,PPX1andPPX2, for PPO-inhibiting herbicides were obtained through the screening of a common ragweed cDNA library and subsequent cDNA extension (5′-RACE). Molecular marker analysis with the F2population revealed that thePPX2gene cosegregated with resistance to PPO-inhibiting herbicides. A mutation substituting an arginine codon for a leucine codon at a conserved location (R98L) of thePPX2gene was suspected of being responsible for resistance. By using a transgenicEscherichia colisystem, it was demonstrated that the R98L mutation was sufficient to confer resistance to PPO-inhibiting herbicides. The level of resistance to acifluorfen conferred by the R98L mutation in theE. colisystem was about 31-fold, similar to the level of resistance seen in the whole-plant dose-response study. Last, a DNA-based assay was developed to identify the presence or absence of the common ragweedPPX2R98L mutation. The R98LPPX2mutation is the second mechanism identified for evolved resistance to PPO-inhibiting herbicides.

scholarly journals PSI-40 Two mitochondrial lineages revealed in North American yak

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 477-477
Author(s):  
Leah K Treffer ◽  
Edward S Rice ◽  
Anna M Fuller ◽  
Samuel Cutler ◽  
Jessica L Petersen
Keyword(s):  
Sequence Data ◽  
Haplotype Network ◽  
Ovis Aries ◽  
Similar Species ◽  
Nucleotide Polymorphisms ◽  
Mt Dna ◽  
Protein Coding ◽  
Sister Clade ◽  
Mtdna Sequence ◽  
The Impact

Abstract Domestic yak (Bos grunniens) are bovids native to the Asian Qinghai-Tibetan Plateau. Studies of Asian yak have revealed that introgression with domestic cattle has contributed to the evolution of the species. When imported to North America (NA), some hybridization with B. taurus did occur. The objective of this study was to use mitochondrial (mt) DNA sequence data to better understand the mtDNA origin of NA yak and their relationship to Asian yak and related species. The complete mtDNA sequence of 14 individuals (12 NA yak, 1 Tibetan yak, 1 Tibetan B. indicus) was generated and compared with sequences of similar species from GeneBank (B. indicus, B. grunniens (Chinese), B. taurus, B. gaurus, B. primigenius, B. frontalis, Bison bison, and Ovis aries). Individuals were aligned to the B. grunniens reference genome (ARS_UNL_BGru_maternal_1.0), which was also included in the analyses. The mtDNA genes were annotated using the ARS-UCD1.2 cattle sequence as a reference. Ten unique NA yak haplotypes were identified, which a haplotype network separated into two clusters. Variation among the NA haplotypes included 93 nonsynonymous single nucleotide polymorphisms. A maximum likelihood tree including all taxa was made using IQtree after the data were partitioned into twenty-two subgroups using PartitionFinder2. Notably, six NA yak haplotypes formed a clade with B. indicus; the other four haplotypes grouped with B. grunniens and fell as a sister clade to bison, gaur and gayal. These data demonstrate two mitochondrial origins of NA yak with genetic variation in protein coding genes. Although these data suggest yak introgression with B. indicus, it appears to date prior to importation into NA. In addition to contributing to our understanding of the species history, these results suggest the two major mtDNA haplotypes in NA yak may functionally differ. Characterization of the impact of these differences on cellular function is currently underway.

scholarly journals Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dimitri Boeckaerts ◽  
Michiel Stock ◽  
Bjorn Criel ◽  
Hans Gerstmans ◽  
Bernard De Baets ◽  
...  
Keyword(s):  
Machine Learning ◽  
Predictive Model ◽  
Receptor Binding ◽  
Bacterial Infections ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Area Under The Curve ◽  
Local Alignment ◽  
Search Tool ◽  
Different Levels

AbstractNowadays, bacteriophages are increasingly considered as an alternative treatment for a variety of bacterial infections in cases where classical antibiotics have become ineffective. However, characterizing the host specificity of phages remains a labor- and time-intensive process. In order to alleviate this burden, we have developed a new machine-learning-based pipeline to predict bacteriophage hosts based on annotated receptor-binding protein (RBP) sequence data. We focus on predicting bacterial hosts from the ESKAPE group, Escherichia coli, Salmonella enterica and Clostridium difficile. We compare the performance of our predictive model with that of the widely used Basic Local Alignment Search Tool (BLAST). Our best-performing predictive model reaches Precision-Recall Area Under the Curve (PR-AUC) scores between 73.6 and 93.8% for different levels of sequence similarity in the collected data. Our model reaches a performance comparable to that of BLASTp when sequence similarity in the data is high and starts outperforming BLASTp when sequence similarity drops below 75%. Therefore, our machine learning methods can be especially useful in settings in which sequence similarity to other known sequences is low. Predicting the hosts of novel metagenomic RBP sequences could extend our toolbox to tune the host spectrum of phages or phage tail-like bacteriocins by swapping RBPs.

unrechtliche peinliche schmehung oder dem gemeinen nutz nuetzlich?Eine Fallstudie zur Normenkonkurrenz im Schmähschriftprozess des 16. Jahrhunderts

2020 ◽  
Vol 25 (1) ◽  
pp. 135-149
Author(s):  
Jan Siegemund
Keyword(s):  
Early Modern ◽  
Common Good ◽  
Public Places ◽  
Legal Norms ◽  
The Public ◽  
The Common ◽  
The Public Sphere ◽  
The City ◽  
Different Levels

AbstractLibel played an important and extraordinary role in early modern conflict culture. The article discusses their functions and the way they were assessed in court. The case study illustrates argumentative spaces and different levels of normative references in libel trials in 16th century electoral Saxony. In 1569, Andreas Langener – in consequence of a long stagnating private conflict – posted several libels against the nobleman Tham Pflugk in different public places in the city of Dresden. Consequently, he was arrested and charged with ‘libelling’. Depending on the reference to conflicting social and legal norms, he had therefore been either threatened with corporal punishment including his execution, or rewarded with laudations. In this case, the act of libelling could be seen as slander, but also as a service to the community, which Langener had informed about potentially harmful transgression of norms. While the common good was the highest maxim, different and sometimes conflicting legally protected interests had to be discussed. The situational decision depended on whether the articulated charges where true and relevant for the public, on the invective language, and especially on the quality and size of the public sphere reached by the libel.

scholarly journals Kelch 13-propeller polymorphisms in Plasmodium falciparum from Jazan region, southwest Saudi Arabia

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Ommer Mohammed Dafalla ◽  
Mohammed Alzahrani ◽  
Ahmed Sahli ◽  
Mohammed Abdulla Al Helal ◽  
Mohammad Mohammad Alhazmi ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Saudi Arabia ◽  
Parasite Clearance ◽  
Sub Saharan Africa ◽  
Local Alignment ◽  
Nucleotide Polymorphisms ◽  
Gene Encoding ◽  
Synonymous Mutations ◽  
Search Tool ◽  
Sub Saharan

Abstract Background Artemisinin-based combination therapy (ACT) is recommended at the initial phase for treatment of Plasmodium falciparum, to reduce morbidity and mortality in all countries where malaria is endemic. Polymorphism in portions of P. falciparum gene encoding kelch (K13)-propeller domains is associated with delayed parasite clearance after ACT. Of about 124 different non-synonymous mutations, 46 have been identified in Southeast Asia (SEA), 62 in sub-Saharan Africa (SSA) and 16 in both the regions. This is the first study designed to analyse the prevalence of polymorphism in the P. falciparum k13-propeller domain in the Jazan region of southwest Saudi Arabia, where malaria is endemic. Methods One-hundred and forty P. falciparum samples were collected from Jazan region of southwest Saudi Arabia at three different times: 20 samples in 2011, 40 samples in 2016 and 80 samples in 2020 after the implementation of ACT. Plasmodium falciparum kelch13 (k13) gene DNA was extracted, amplified, sequenced, and analysed using a basic local alignment search tool (BLAST). Results This study obtained 51 non-synonymous (NS) mutations in three time groups, divided as follows: 6 single nucleotide polymorphisms (SNPs) ‘11.8%’ in samples collected in 2011 only, 3 (5.9%) in 2011and 2016, 5 (9.8%) in 2011 and 2020, 5 (9.8%) in 2016 only, 8 (15.7%) in 2016 and 2020, 14 (27.5%) in 2020 and 10 (19.6%) in all the groups. The BLAST revealed that the 2011 isolates were genetically closer to African isolates (53.3%) than Asian ones (46.7%). Interestingly, this proportion changed completely in 2020, to become closer to Asian isolates (81.6%) than to African ones (18.4%). Conclusions Despite the diversity of the identified mutations in the k13-propeller gene, these data did not report widespread artemisinin-resistant polymorphisms in the Jazan region where these samples were collected. Such a process would be expected to increase frequencies of mutations associated with the resistance of ACT.

scholarly journals Association between EFHD2 gene polymorphisms and schizophrenia among the Han population in northern China

2020 ◽  
Vol 48 (6) ◽  
pp. 030006052093280
Author(s):  
Meng Gao ◽  
Kuo Zeng ◽  
Ya Li ◽  
Yong-ping Liu ◽  
Xi Xia ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Neurodevelopmental Disorder ◽  
Haplotype Frequency ◽  
Northern China ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphisms ◽  
Chinese Han ◽  
Gene Encoding ◽  
Frequency Distributions ◽  
And Control

Objective Schizophrenia is a severe neurodevelopmental disorder with a complex genetic and environmental etiology. The gene encoding EF-hand domain-containing protein D2 ( EFHD2) may be a genetic risk locus for schizophrenia. Methods We genotyped four EFHD2 single-nucleotide polymorphisms (281 schizophrenia cases [SCZ], 321 controls) from northern Chinese Han individuals using Sanger sequencing and polymerase chain reaction-restriction fragment length polymorphism analysis. Differences existed in genotype, allele, and haplotype frequency distributions between SCZ and control groups. Results The rs2473357 genotype and allele frequency distributions differed between SCZ and controls; however, this difference disappeared after Bonferroni correction. Differences in rs2473357 genotype and allele frequency distributions between SCZ and controls were more pronounced in men than in women. The G allele increased schizophrenia risk (odds ratio = 1.807, 95% confidence interval = 1.164–2.803). Among six haplotypes (G–, A–, G-insC, A-C, G-C, and G-T), the G– haplotype frequency distribution differed between SCZ and controls in women; the A-C and G-C haplotype frequency distributions differed between SCZ and controls in men. Conclusions EFHD2 may be involved in schizophrenia. Sex differences in EFHD2 genotype and allele frequency distributions existed among schizophrenia patients. Further research is needed to determine the role of EFHD2 in schizophrenia.

scholarly journals A NOTE ON PHASING LONG GENOMIC REGIONS USING LOCAL HAPLOTYPE PREDICTIONS

2006 ◽  
Vol 04 (03) ◽  
pp. 639-647 ◽  
Author(s):  
ELEAZAR ESKIN ◽  
RODED SHARAN ◽  
ERAN HALPERIN
Keyword(s):  
Large Scale ◽  
Computational Cost ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Novel Approach ◽  
Maximum Likelihood Criterion ◽  
The Common ◽  
Genomic Regions ◽  
High Computational Cost ◽  
Combining Information

The common approaches for haplotype inference from genotype data are targeted toward phasing short genomic regions. Longer regions are often tackled in a heuristic manner, due to the high computational cost. Here, we describe a novel approach for phasing genotypes over long regions, which is based on combining information from local predictions on short, overlapping regions. The phasing is done in a way, which maximizes a natural maximum likelihood criterion. Among other things, this criterion takes into account the physical length between neighboring single nucleotide polymorphisms. The approach is very efficient and is applied to several large scale datasets and is shown to be successful in two recent benchmarking studies (Zaitlen et al., in press; Marchini et al., in preparation). Our method is publicly available via a webserver at .

Extracting a needle from a haystack: reanalysis of whole genome data reveals a readily translatable finding

2009 ◽  
Vol 39 (8) ◽  
pp. 1231-1235 ◽  
Author(s):  
R. Keers ◽  
A. E. Farmer ◽  
K. J. Aitchison
Keyword(s):  
Bipolar Disorder ◽  
Calcium Channel ◽  
Unmet Need ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Gene Encoding ◽  
Genome Data ◽  
Early Results ◽  
Genome Association ◽  
Genome Study

There is significant unmet need for more effective treatments for bipolar disorder. The drug discovery process is becoming prohibitively expensive. Hence, biomarker clues to assist or shortcut this process are now widely sought. Using the publicly available data from the whole genome association study conducted by the Wellcome Trust Case Control Consortium, we sought to identify groups of genetic markers (single nucleotide polymorphisms) in which each marker was independently associated with bipolar disorder, with a less stringent threshold than that set by the original investigators (p⩽1×10−4). We identified a group of markers occurring within the CACNA1C gene (encoding the alpha subunit of the calcium channel Cav1.2). We then ascertained that this locus had been previously associated with the disorder in both a smaller and a whole genome study, and that a number of drugs blocking this channel (including verapamil and diltiazem) had been trialled in the treatment of bipolar disorder. The dihydropyridine-based blockers such as nimodipine that bind specifically to Cav1.2 and are more penetrant to the central nervous system have shown some promising early results; however, further trials are indicated. In addition, migraine is commonly seen in affective disorder, and calcium channel antagonists are successfully used in the treatment of migraine. One such agent, flunarizine, is structurally related to other first-generation derivatives of antihistamines such as antipsychotics. This implies that flunarizine could be useful in the treatment of bipolar disorder, and, furthermore, that other currently licensed drugs should be investigated for antagonism of Cav1.2.

148 Multiple Dysregulated Novel Pathways and Genes in Aleutian Mink Disease Revealed by Selection Signatures and Gene Network Analyses Using Whole-genome Sequence Data

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 76-76
Author(s):  
Seyed Milad Vahedi ◽  
Karim Karimi ◽  
Siavash Salek Ardestani ◽  
Younes Miar
Keyword(s):  
Sequence Data ◽  
American Mink ◽  
Enrichment Analysis ◽  
Whole Genome Sequence ◽  
Fixation Index ◽  
Pathway Enrichment Analysis ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Network Analyses ◽  
Genome Level

Abstract Aleutian disease (AD) is a chronic persistent infection in domestic mink caused by Aleutian mink disease virus (AMDV). Female mink’s fertility and pelt quality depression are the main reasons for the AD’s negative economic impacts on the mink industry. A total number of 79 American mink from the Canadian Center for Fur Animal Research at Dalhousie University (Truro, NS, Canada) were classified based on the results of counter immunoelectrophoresis (CIEP) tests into two groups of positive (n = 48) and negative (n = 31). Whole-genome sequences comprising 4,176 scaffolds and 8,039,737 single nucleotide polymorphisms (SNPs) were used to trace the selection footprints for response to AMDV infection at the genome level. Window-based fixation index (Fst) and nucleotide diversity (θπ) statistics were estimated to compare positive and negative animals’ genomes. The overlapped top 1% genomic windows between two statistics were considered as potential regions underlying selection pressures. A total of 98 genomic regions harboring 33 candidate genes were detected as selective signals. Most of the identified genes were involved in the development and functions of immune system (PPP3CA, SMAP2, TNFRSF21, SKIL, and AKIRIN2), musculoskeletal system (COL9A2, PPP1R9A, ANK2, AKAP9, and STRIT1), nervous system (ASCL1, ZFP69B, SLC25A27, MCF2, and SLC7A14), reproductive system (CAMK2D, GJB7, SSMEM1, C6orf163), liver (PAH and DPYD), and lung (SLC35A1). Gene-expression network analysis showed the interactions among 27 identified genes. Moreover, pathway enrichment analysis of the constructed genes network revealed significant oxytocin (KEGG: hsa04921) and GnRH signaling (KEGG: hsa04912) pathways, which are likely to be impaired by AMDV leading to dams’ fecundity reduction. These results provided a perspective to the genetic architecture of response to AD in American mink and novel insight into the pathogenesis of AMDV.

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