scholarly journals Phenotypic and Molecular Identification of Pathogenic Fusarium Species Isolated from Various Pulse Growing Geographic Areas of India

2021 ◽  
Vol 10 (11) ◽  
pp. 120-132
Author(s):  
Monika Singh O. P. Sharma ◽  
Someshwar Bhagat
Keyword(s):  
Molecular Identification ◽  
Dna Sequences ◽  
Fusarium Species ◽  
Economic Loss ◽  
Colony Growth ◽  
Likelihood Method ◽  
Multiple Sequence ◽  
Colony Color ◽  
Fusarium Sp ◽  
Its Dna Sequences

Fusarium phythopathogenic fungi is responsible for high economic loss of cereal food crop. The objective of this study was aimed at isolation, morphological and molecular identification of Fusarium species. 13 different Fusarium spp. i.e. F. solani, F. chlamydosporum, F. tabacinum, F. fujikuroi, F. oxysporum, F. verticillioides, F. brachygibbosum, Fusarium sp. and F. incarnatum were isolated and identified from diseased samples of chickpea, pigeonpea, rice, lentil and garden pea crop. Colony characteristics like colony color, colony growth diameters, mycelium type, sporulation, pigmentation, odour were obtained after culture purification. Shape, size and septation of microconidia and macroconidia, position, shape, occurrence and size of chlamydospores, conidiophore branching were examined microscopically. MS10, BI01 and KA14 isolates were slow growing, BI02 and UP07 were moderate growing and BI03, HA04, MS06, MS09, MS11 and KA(Gul)13 were fast to very fast growing on PDA after 7-10 days. Chlamydospores were found in most of the isolates. Colonies were abundant, loosely tufted, fluffy, pannose, vinaceous floccose, powdery and some were flat appressed, arachnoid. Pigmentation of most of the isolates was pinkish white to dark pink, carmine to violet in colour. Phylogenetic analysis was done by maximum likelihood method using the ITS-rDNA region of Fusarium isolates and multiple sequence alignment of ITS DNA sequences was done using Clustal_W program and all identified sequences were submitted in NCBI GenBank database.

scholarly journals Mango Malformation Disease and the Associated Fusarium Species

2006 ◽  
Vol 96 (6) ◽  
pp. 667-672 ◽  
Author(s):  
W. F. O. Marasas ◽  
R. C. Ploetz ◽  
M. J. Wingfield ◽  
B. D. Wingfield ◽  
E. T. Steenkamp
Keyword(s):  
South Africa ◽  
Dna Sequences ◽  
Fusarium Species ◽  
Floral Tissue ◽  
Sexual Compatibility ◽  
Fusarium Sp ◽  
Floral Form ◽  
Mango Malformation ◽  
A New Species ◽  
Gibberella Intermedia

Mango malformation disease (MMD) occurs in Asia, Africa, and the Americas and was first reported in India in 1891. The vegetative form of MMD was first reproduced in 1966 with Fusarium moniliforme and the floral form with isolates of F. moniliforme var. subglutinans from both vegetative shoots and floral tissue. The fungi were subsequently recognized as F. subglutinans. In 2002, a new species, F. mangiferae, was established based on nuclear and mitochondrial DNA sequences; it included strains of F. subglutinans from Egypt, Florida, Israel, Malaysia, and South Africa, some of which had been shown to cause MMD by artificial inoculation. At least three additional taxa have been associated with MMD: F. sterilihyphosum from Brazil and South Africa, and Fusarium sp. nov. and F. proliferatum (teleomorph: Gibberella intermedia) from Malaysia. To date, Koch's postulates have not been completed with them. In the future, gene sequencing will be essential to identify the Fusarium spp. that are associated with MMD. Work remains to be done on the morphology, sexual compatibility, pathogenicity, and toxigenicity of these taxa.

Deoxyribonucleic Acid as a Tool for Digital Information Storage: An Overview

2019 ◽  
Vol 15 (01) ◽  
pp. 1-8
Author(s):  
Ashish C Patel ◽  
C G Joshi
Keyword(s):  
Data Storage ◽  
Dna Sequences ◽  
Consensus Sequence ◽  
Random Access ◽  
Information Storage ◽  
Digital Data ◽  
Digital Information ◽  
Multiple Sequence ◽  
Digital World ◽  
Digital File

Current data storage technologies cannot keep pace longer with exponentially growing amounts of data through the extensive use of social networking photos and media, etc. The "digital world” with 4.4 zettabytes in 2013 has predicted it to reach 44 zettabytes by 2020. From the past 30 years, scientists and researchers have been trying to develop a robust way of storing data on a medium which is dense and ever-lasting and found DNA as the most promising storage medium. Unlike existing storage devices, DNA requires no maintenance, except the need to store at a cool and dark place. DNA has a small size with high density; just 1 gram of dry DNA can store about 455 exabytes of data. DNA stores the informations using four bases, viz., A, T, G, and C, while CDs, hard disks and other devices stores the information using 0’s and 1’s on the spiral tracks. In the DNA based storage, after binarization of digital file into the binary codes, encoding and decoding are important steps in DNA based storage system. Once the digital file is encoded, the next step is to synthesize arbitrary single-strand DNA sequences and that can be stored in the deep freeze until use.When there is a need for information to be recovered, it can be done using DNA sequencing. New generation sequencing (NGS) capable of producing sequences with very high throughput at a much lower cost about less than 0.1 USD for one MB of data than the first sequencing technologies. Post-sequencing processing includes alignment of all reads using multiple sequence alignment (MSA) algorithms to obtain different consensus sequences. The consensus sequence is decoded as the reversal of the encoding process. Most prior DNA data storage efforts sequenced and decoded the entire amount of stored digital information with no random access, but nowadays it has become possible to extract selective files (e.g., retrieving only required image from a collection) from a DNA pool using PCR-based random access. Various scientists successfully stored up to 110 zettabytes data in one gram of DNA. In the future, with an efficient encoding, error corrections, cheaper DNA synthesis,and sequencing, DNA based storage will become a practical solution for storage of exponentially growing digital data.

scholarly journals Thermodynamic Model for B-Z Transition of DNA Induced by Z-DNA Binding Proteins

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2748 ◽  
Author(s):  
Ae-Ree Lee ◽  
Na-Hyun Kim ◽  
Yeo-Jin Seo ◽  
Seo-Ree Choi ◽  
Joon-Hwa Lee
Keyword(s):  
Dna Binding ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Multiple Sequence ◽  
Left Handed ◽  
Transition Mechanism ◽  
Dna Strands ◽  
Z Dna

Z-DNA is stabilized by various Z-DNA binding proteins (ZBPs) that play important roles in RNA editing, innate immune response, and viral infection. In this review, the structural and dynamics of various ZBPs complexed with Z-DNA are summarized to better understand the mechanisms by which ZBPs selectively recognize d(CG)-repeat DNA sequences in genomic DNA and efficiently convert them to left-handed Z-DNA to achieve their biological function. The intermolecular interaction of ZBPs with Z-DNA strands is mediated through a single continuous recognition surface which consists of an α3 helix and a β-hairpin. In the ZBP-Z-DNA complexes, three identical, conserved residues (N173, Y177, and W195 in the Zα domain of human ADAR1) play central roles in the interaction with Z-DNA. ZBPs convert a 6-base DNA pair to a Z-form helix via the B-Z transition mechanism in which the ZBP first binds to B-DNA and then shifts the equilibrium from B-DNA to Z-DNA, a conformation that is then selectively stabilized by the additional binding of a second ZBP molecule. During B-Z transition, ZBPs selectively recognize the alternating d(CG)n sequence and convert it to a Z-form helix in long genomic DNA through multiple sequence discrimination steps. In addition, the intermediate complex formed by ZBPs and B-DNA, which is modulated by varying conditions, determines the degree of B-Z transition.

scholarly journals Cross-border Investigations on the Prevalence and Transmission Dynamics of Cryptosporidium Species in Dairy Cattle Farms in Western Mainland Europe

2021 ◽  
Author(s):  
Pedro Pinto ◽  
Claudia A Ribeiro ◽  
Sumaiya Hoque ◽  
Ourida Hammouma ◽  
Hélène Leruste ◽  
...  
Keyword(s):  
The Netherlands ◽  
Human Health ◽  
Dna Sequences ◽  
Significant Risk ◽  
Dairy Farms ◽  
Economic Loss ◽  
Cryptosporidium Spp ◽  
Wide Range ◽  
Parasitic Protist ◽  
Cattle Farms

Cryptosporidium is comprised an apicomplexan parasitic protist, which infects a wide range of hosts, causing cryptosporidiosis. In cattle farms, the incidence of cryptosporidiosis results in high mortality in calves leading to considerable economic loss in the livestock industry. Infected animals may also act as a major reservoir of Cryptosporidium spp., in particular C. parvum, the most common cause of cryptosporidiosis in calves. This poses a significant risk to other farms via breeding centres, to trading of livestock and to human health. This study, funded by the Interreg-2-seas programme, is a part of a global project aimed at strategies to tackle cryptosporidiosis. To reach this target, it was essential to determine whether prevalence was dependent on the studied countries or if the issue was borderless. Indeed, C. parvum occurrence was assessed across dairy farms in certain regions of Belgium, France and the Netherlands. At the same time, the animal-to-animal transmission of the circulating C. parvum subtypes was studied. To accomplish this, 1084 faecal samples, corresponding to 57 dairy-farms from all three countries, were analysed. Well-established protocols amplifying the 18S rDNA and gp60 genes fragments, followed by DNA sequencing, were used for the detection and subtyping C. parvum; the DNA sequences obtained were further characterised using a combination of bioinformatics and phylogenetics methods. Our results show 25.7%, 24.9% and 20.8% prevalence of Cryptosporidium spp. in Belgium, France and the Netherlands respectively. Overall, 93% of the farms were Cryptosporidium positive. The gp60 subtyping demonstrated a significant number of the C. parvum positives belonged to the IIa allelic family, which has been also detected in humans. Consequently, this study highlights how widespread is C. parvum in dairy farms and endorses cattle as a major carrier of zoonotic C. parvum subtypes, which subsequently pose a significant threat to human health.

scholarly journals Model-based inference of punctuated molecular evolution

2019 ◽  
Author(s):  
Marc Manceau ◽  
Julie Marin ◽  
Hélène Morlon ◽  
Amaury Lambert
Keyword(s):  
Molecular Evolution ◽  
Dna Sequences ◽  
Temporal Variations ◽  
Multiple Sequence ◽  
Model Combining ◽  
Constant Rate ◽  
Whole Genomes ◽  
Standard Models ◽  
Natural Variance ◽  
Venom Proteins

AbstractIn standard models of molecular evolution, DNA sequences evolve through asynchronous substitutions according to Poisson processes with a constant rate (called the molecular clock) or a time-varying rate (relaxed clock). However, DNA sequences can also undergo episodes of fast divergence that will appear as synchronous substitutions affecting several sites simultaneously at the macroevolutionary time scale. Here, we develop a model combining basal, clock-like molecular evolution with episodes of fast divergence called spikes arising at speciation events. Given a multiple sequence alignment and its time-calibrated species phylogeny, our model is able to detect speciation events (including hidden ones) co-occurring with spike events and to estimate the probability and amplitude of these spikes on the phylogeny. We identify the conditions under which spikes can be distinguished from the natural variance of the clock-like component of molecular evolution and from temporal variations of the clock. We apply the method to genes underlying snake venom proteins and identify several spikes at gene-specific locations in the phylogeny. This work should pave the way for analyses relying on whole genomes to inform on modes of species diversification.

scholarly journals Efficient Maximum-Likelihood Inference For The Isolation-With-Initial-Migration Model With Potentially Asymmetric Gene Flow

2016 ◽  
Author(s):  
Rui J. Costa ◽  
Hilde Wilkinson-Herbots
Keyword(s):  
Gene Flow ◽  
Maximum Likelihood ◽  
Dna Sequences ◽  
Computing Time ◽  
Likelihood Method ◽  
Ancestral Population ◽  
Parameter Estimates ◽  
Fast Method ◽  
Data Set ◽  
Im Model

AbstractThe isolation-with-migration (IM) model is commonly used to make inferences about gene flow during speciation, using polymorphism data. However, Becquet and Przeworski (2009) report that the parameter estimates obtained by fitting the IM model are very sensitive to the model's assumptions (including the assumption of constant gene flow until the present). This paper is concerned with the isolation-with-initial-migration (IIM) model of Wilkinson-Herbots (2012), which drops precisely this assumption. In the IIM model, one ancestral population divides into two descendant subpopulations, between which there is an initial period of gene flow and a subsequent period of isolation. We derive a very fast method of fitting an extended version of the IIM model, which also allows for asymmetric gene flow and unequal population sizes. This is a maximum-likelihood method, applicable to data on the number of segregating sites between pairs of DNA sequences from a large number of independent loci. In addition to obtaining parameter estimates, our method can also be used to distinguish between alternative models representing different evolutionary scenarios, by means of likelihood ratio tests. We illustrate the procedure on pairs of Drosophila sequences from approximately 30,000 loci. The computing time needed to fit the most complex version of the model to this data set is only a couple of minutes. The R code to fit the IIM model can be found in the supplementary files of this paper.

Multiple functional motifs in the chicken U1 RNA gene enhancer

1987 ◽  
Vol 7 (12) ◽  
pp. 4185-4193
Author(s):  
K A Roebuck ◽  
R J Walker ◽  
W E Stumph
Keyword(s):  
Gene Expression ◽  
Dna Sequences ◽  
Initiation Site ◽  
Sequence Motifs ◽  
Small Nuclear Rna ◽  
Multiple Sequence ◽  
Transcriptional Initiation ◽  
Transcription System ◽  
Cell Extracts ◽  
Gene Enhancer

The DNA sequence requirements of chicken U1 RNA gene expression have been examined in an oocyte transcription system. An enhancer region, which was required for efficient U1 RNA gene expression, is contained within a region of conserved DNA sequences spanning nucleotide positions -230 to -183, upstream of the transcriptional initiation site. These DNA sequences can be divided into at least two distinct subregions or domains that acted synergistically to provide a greater than 20-fold stimulation of U1 RNA synthesis. The first domain contains the octamer sequence ATGCAAAT and was recognized by a DNA-binding factor present in HeLa cell extracts. The second domain (the SPH domain) consists of conserved sequences immediately downstream of the octamer and is an essential component of the enhancer. In the oocyte, the DNA sequences of the SPH domain were able to enhance gene expression at least 10-fold in the absence of the octamer domain. In contrast, the octamer domain, although required for full U1 RNA gene activity, was unable to stimulate expression in the absence of the adjacent downstream DNA sequences. These findings imply that sequences 3' of the octamer play a major role in the function of the chicken U1 RNA gene enhancer. This concept was supported by transcriptional competition studies in which a cloned chicken U4B RNA gene was used to compete for limiting transcription factors in oocytes. Multiple sequence motifs that can function in a variety of cis-linked configurations may be a general feature of vertebrate small nuclear RNA gene enhancers.

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